Gene Expression

Bing vs. Google  permlink

Category: Technology

Two positive assessments of Bing. Google is my main search engine, but I use Bing's image search preferentially now since the UI seems less kludgey.

Posted by Razib at 2:24 PM • 0 Comments

Uighurs & China  permlink

Category: Culture • History

Over at Accidental Blogger a remembrance of travels in Xinjiang/East Turkestan. I think the best model for what's going on in China right now is a race riot catalyzed by economic resentment. Uighurs seem to be attacking Hui as well as Han, the Hui being Chinese speakers who are of Muslim background (and by and large are physically indistinguishable from the Han, for example, the Vice Premier of China is a Hui).. Though China is still a poor country much of it is lurching toward modernity; the Uighurs of Xinjiang are an exception to this trend.

Related: Post from last year.

Posted by Razib at 12:31 PM • 0 Comments

Our god the state  permlink

Category: Culture

Tom Rees of Epiphenom has a new paper out, Is Personal Insecurity a Cause of Cross-National Differences in the Intensity of Religious Belief?. The abstract:

Previous research has shown an apparent relationship between "societal health" and religiosity, with nations that exhibit higher mean personal religiosity also tending to provide worse social environments. A possible cause is that exposure to stressful situations (i.e. personal insecurity) increases personal religiosity. To test this hypothesis, income inequality, a widely available proxy for personal insecurity, was compared with other macro-scale causes of religiosity (derived from modernization and rational choice theories) in a multinational, cross-sectional analysis. Income inequality, and hence personal insecurity, was found to be an important determinant of religiosity in this diverse sample of nations.

Rees explores the paradox that though within nations those who are religious tend to be more prosocial, between nations those with higher fractions of very religious individuals tend to exhibit more anomie. Here is for example a map of world happiness which has been circulating recently:

The richest nations in the world tend to be more secular, and also happen to have higher median happiness. But within those nations the religious are often the happiest. Rees' thesis is most succinctly presented in a chart (reedited for width):

Read on »

Posted by Razib at 8:33 AM • 0 Comments

Elite Republicans & Democrats vs. the masses  permlink

Category: Culture

Over at Secular Right I break down attitudes toward a host of issues as a function of class and party identification. It is interesting to see the issues where class matters more than party, and those where party matters more than class, and where one segment is an outlier. Below the fold are a few questions of possible specific interest to ScienceBlogs readers.

Read on »

Posted by Razib at 3:03 PM • 3 Comments

Around ScienceBlogs  permlink

Category: Blog • Culture

Sunday Function

The subsidiary patient

Pavlov's Dogs: Proving the Null With Bayesianism

UK House of Lords report on genomic medicine: implications for DTC genetic testing

More fuss over Enceladus

Posted by Razib at 10:32 AM • 0 Comments

Get your "beta" back on  permlink

Category: Technology

Gmail and a raft of other apps were finally thrown out of beta recently. The assumed reason is that Google is trying to horn in on the enormous business market for applications, and people can get fired for greenlighting betas which break. But if you miss that not-ready-for-primetime new app feel, go "Back to Beta".

Posted by Razib at 2:41 AM • 1 Comments

Population genomics & the coalescent  permlink

Category: Culture • Genetics

Blogger Thomas Mailund is an author on a new paper, Ancestral Population Genomics: The Coalescent Hidden Markov Model Approach:

With incomplete lineage sorting (ILS), the genealogy of closely related species differs along their genomes. The amount of ILS depends on population parameters such as the ancestral effective population sizes and the recombination rate, but also on the number of generations between speciation events. We use a hidden Markov model parametrized according to coalescent theory in order to infer the genealogy along a four-species genome alignment of closely related species, and estimate population parameters. We analyze a basic, panmictic demographic model and study its properties using an extensive set of coalescent simulations. We assess the effect of the model assumptions, and demonstrate that the Markov property provides a good approximation to the ancestral recombination graph. Using a too restricted set of possible genealogies, necessary to reduce the computational load, can bias parameter estimates. We propose a simple correction for this bias, and suggest directions for future extensions of the model. We show that the patterns of ILS along a sequence alignment can be recovered efficiently together with the ancestral recombination rate. Finally, we introduce an extension of the basic model that allows for mutation rate heterogeneity, and reanalyze Human-Chimpanzee-Gorilla-Orangutan alignments using the new models. We expect that this framework will prove useful for population genomics and provide exciting insights into genome evolution.

Posted by Razib at 2:28 AM • 1 Comments

Folk wanderings in "the Heartland"  permlink

Category: Genetics

In the early 20th century the geographer Halford Mackinder posited that the key to world domination lay in the control of the Eurasian Heartland. This was in sharp contrast to Alfred Mahan's emphasis on the role of naval power. Whatever the applicability of these geopolitical frameworks in the modern era, it is interesting to observe their precedents in the ancient and medieval world. The rise of Rome was facilitated by the Mediterranean essential role as a conduit for communication and trade which connected the cities which were the foci of the Empire. Easy transport of cheap grain from Egypt or Sicily to Rome or Constantinople allowed these cities to scale up to enormous proportions. In contrast Han China did not have the advantage of the same natural endowments of water transport, which might explain the greater emphasis on primary production and local provisioning within the Chinese state. But after the fall of Rome and Han China Eurasia witnessed the first of repeated eruptions from the steppe of nomadic peoples. In the West the Huns and Avars stitched together diverse confederacies predicated on extracting rents from the shrunken post-Roman world. In the East the heirs of the Xiongnu swept over the North China plain, and drove the Han elite south of the Yangtze. In the 6th century there arose a Turk empire which stretched from the Caspian to Manchuria, the collapse of which sent the various tribes streaming across the frontiers of what was at the time becoming the Islamic world. The subsequent rise of the Mongols is well known, the last and most ferocious in a long line of roving nomadic bands whose power was finally checked only by the rise of gunpowder states.

But the period between 500 and 1500 A.D. is only a thin slice of history, and does not reflect the whole story. Herodotus tells us of the Scythians, who ravaged the Middle East and Europe. The Romans later defeated Sarmatians on the plains of Pannonia. Even further back in history we know of the Indo-Aryan Mittani in Syria, while there are hints of a relationship between nomadic societies on the steppe of Eurasia and later settled populations in Eastern Europe, Iran & India. Because of the lack of literacy in most of the world before 500 B.C. we must rely on archaeology to connect the vaguest of these dots. But the new field of ancient DNA allows us to go a step beyond "Pots not Peoples" and reconstruct phylogenies across space and time.

Two new papers address some issues relating to the Eurasian Heartland and its genetic history, Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis and Ancient DNA provides new insights into the history of south Siberian Kurgan people. There is a great deal of overlap in the substance and data because the same groups produced these two papers. Here are the abstracts:

Read on »

Posted by Razib at 8:15 AM • 9 Comments

Voyage to Antarctica  permlink

Category: Blog

Living the Scientific Life is still in the running for the trip to Antarctica. If you haven't, consider voting for her essay.

Posted by Razib at 4:28 PM • 0 Comments

How tall will Megan McArdle & Peter Suderman's theoretical offspring be?  permlink

Category: Blog

Peter Suderman & Megan McArdle are getting married. One of my thoughts was, "How tall will their offspring be?" (assuming they are intent on producing any) I couldn't tell Peter Suderman's height from photographs with certainty, but he has confirmed they are the same height, 6 feet 2 inches. What sort of heights would we expect for the McSuderkinder?* Assuming 80% heritability for height, 3 inches as the standard deviation for both sexes, 5'10 and 5'4 as mean heights (male & female), and plugging into the calculator:

Read on »

Posted by Razib at 12:54 PM • 6 Comments

Attitudes about evolution across countries  permlink

Category:

I have posted Creationism as a function of geography before. John Lynch pointed me to a new poll of Argentina, China, Egypt, Great Britain, India, Mexico, Russia, South Africa, Spain and the USA. Though the set of countries is smaller than in some surveys, the number of questions asked were much larger:

-Heard of Darwin
-Not Heard of Darwin
-Know a good/fair amount Know a little/not much
-Know nothing
-Agree that scientific evidence for evolution exists
-Do not think there is scientific evidence for evolution
-Neither agree nor disagree there is scientific evidence for evolution
-Think it is possible to believe in a God and evolution simultaneously
-Think it is NOT possible to believe in God and evolution simultaneously
-Neither agree nor disagree that it is possible to believe in God and evolution
-Think only evolution should be taught in education
-Think evolution should be taught alongside other theories
-Think evolution should NOT be taught, only other theories
-No theories at all should be taught
-No Opinion

You can see the results at the link above. It also turns out that all the nations listed are represented in the 2005 World Values Survey, so one can compare the responses to variables in that data set. So I looked at the variable "God Very Important," with the frequency who said it was "very important" and added it as a column. Additionally, many of the questions have alternatives which add up to less than 100% because only a subset of the respondents would be able to answer them (those who "Heard of Darwin"). I normalized these results so that they added up to 100% (e.g., so really 40% of people who have Heard of Darwin might agree that scientific evidence for evolution exsts).

Comparing the relationships between the columns I selected a few that I thought were interesting, mostly to see where on the chart the nations cluster.

Read on »

Posted by Razib at 4:38 AM • 6 Comments

Desktop blogging  permlink

Category: Blog

An Index Of Blogging Clients:

Blogging clients allow you to prepare posts and then upload them directly. Useful for

-composing drafts of posts offline
-easier editing of HTML
-easier inserting and handling of photos
-easier editing of existing posts

Here's a list of the ones I know of. Any additions welcome.

Posted by Razib at 9:04 PM • 1 Comments

The Illumina whole-genome-sequence  permlink

Category: Genetics • Health

I notice that Fortune has a story on personal genomics up, Genetic sequencing gets personal Biotech firm Illumina will sequence your entire genetic code -- and throw in a Mac -- for $48,000:

So far, personalized genomics make up just a small fraction of Illumina's revenue. High costs keep sequencing out of reach for most people. But prices will fall substantially as the technology improves. In fact experts say costs could reach $1000 within three to five years, making more people privy to their entire genetic code.

...

One area Illumina is not diving into is sequence analysis. Instead, it is partnering with genomics companies Navigenics, 23andMe, deCODE Genetics (DCGN), and Knome, which are developing platforms to decipher the data generated by Illumina. So far, the partners are keeping mum on how much they plan to charge the customers Illumina sends their way. Based on the costs of their current genotyping services, prices could range from a few hundred to a few thousand dollars.

Dan MacArthur covered the Illumina story last month in more depth.

Posted by Razib at 3:50 PM • 0 Comments

Hornet vs. bee; insect wars  permlink

Category: Ecology

Many of you might have seen this video of Japanese bees defending their nest against giant hornets:

The Japanese bees swarm and bake the giant hornets. But Ed Young reports that there is more to this story.

Posted by Razib at 3:43 PM • 1 Comments

I don't get political punditry  permlink

Category: Culture

Palin's Move Shocks G.O.P. and Leaves Future Unclear:

Many Republican strategists have argued that it would be difficult for someone to run for governor in 2010 and turn around immediately, while running a state, and run for president in 2012. Gov. Tim Pawlenty of Minnesota announced last month that he would not seek re-election when his term expired in 2010, as he considers a race for president.

George W. Bush was reelected in Texas in 1998 and ran for president in 2000. Is that so exceptional? Or are there other variables at play? And if so, why is this variable so important? (I've seen this assertion elsewhere) I'm not steeped in political history, but I note that F.D.R. won the governor's mansion of New York in 1930, before running for president in 1932.

It seems in regard to Sarah Palin no one really knows what's going on right now. So all the speculation and analysis reminds me of someone who didn't do background reading for their final in class bluebook test and is producing a stream of total crap in the hopes that the professor will deign to pass them.

Posted by Razib at 11:01 AM • 5 Comments