Since I need to attend to non-internet related activities I thought I would leave this open thread for bugs, questions, etc. Seems like something happened to the feed within the past few hours, though it will be fixed soon. Thanks for understanding!

If you are like me, and if you are reading this weblog there is a significant probability you are like me, you read L. L. Cavalli-Sforza‘s History and Geography of Human Genes in the 1990s, and in the early aughts Spencer Wells’ A Journey of Man. Science has come very far in the last in the last 10-15 years, even Cavalli-Sforza’s magnum opus pales in comparison to the literal tsunami of data and analysis which the “post-genomic era” has ushered in. Instead of a gene here and there, or even the mtDNA and Y chromosome, researchers are now looking at hundreds of thousands of genetic variants, SNPs, across genomes. We’re rapidly approaching the era of whole genome sequencing, even if we’re not quite there yet.

But what’s the purpose of advances in technique and computation? Though the long-term project is to understand human variation and genetic function so as to have biomedical utility, in the short-term there is an enormous wealth of more abstract population genetic insight which can be extracted. Because of the biomedical focus of contemporary genomics we take a somewhat anthropocentric view, which is fine by me as I am an unregenerate speciest. The fish, fowl and crawling things of the earth can come later. And in any case, the beauty of the human focus of modern evolutionary genomics is that there are whole disciplines such as paleoanthropology which can serve as partners in interdisciplinary projects.

Humans are like any other organism, buffeted by conventional evolutionary genetic dynamics, drift, migration, natural selection, as well as processes which are more biophysically rooted such as recombination and mutation. Each of these processes leave their tell-tale marks on the genome. Mutation replenishes variation which drift and selection often eliminate, the former by chance and the latter in the form of negative selection. Migration serves to homogenize across populations through gene flow, while diversifying within populations by introducing novel variants. Finally, recombination breaks up linear associations of genetic variants along a DNA sequence, and has been used to explain sex.

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Compliments back at you Ms. Kirshenbaum. Short time no see! Now let’s get the party started. I’ll let Carl go first, since he’s a wild-man.

They review the past 14 years.

If you’re a regular reader of my blogs, you don’t need to go any further. Otherwise, read on….

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This article at The Jury Expert serves as a nice review of literature. Here’s their summary:

Atheists are unique and individual (just like all of us) and we have to attend to the attitudes, beliefs and life experiences that all of us (even atheists) bring to the table as jurors. Conversely, jurors need to be reminded, if they know they are judging an atheist, that they are human, American, and as deserving of thoughtful consideration as we all are. Do you want atheists on your particular jury? It depends. As we mentioned earlier, you probably don’t want a militant atheist–like most militants they are likely too unpredictable and a potentially polarizing force in the deliberation room. (We have seen occasions where juries–and even focus groups–have begun their deliberations with a group prayer. Many atheists (and others) would be very uncomfortable about this, of course, and resistance might have a strong impact on the deliberative process. Of course, if you want a contentious deliberation or a hung jury you may choose to inject a militant atheist, but we aren’t getting into that for this article.)

Most important, maintain an awareness of the intense bias atheism arouses in most Americans, and remember that all bias stems from beliefs, and the trigger is not always a characteristic visible to the eye.

Yes. We are human 🙂

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia:

With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined…the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans….

The tree gets bushier? Just see John Hawks and Carl Zimmer.

That’s all I have to say to Eric Michael Johnson’s post, Ann Coulter, Hate Speech, and Free Societies. OK, seriously, from what I recall Eric is an American, though resident in the forgotten north. American absolutist stances on free speech are not shared by most Western societies, so demanding total free speech is quixotic and culturally tone deaf. Granted, Europe or Canada are not barbaric like China or Muslim societies when it comes to speech, so that communication about this issue is possible. But here are the exceptions to free speech enumerated in the European Convention on Human Rights:

The exercise of these freedoms, since it carries with it duties and responsibilities, may be subject to such formalities, conditions, restrictions or penalties as are prescribed by law and are necessary in a democratic society, in the interests of national security, territorial integrity or public safety, for the prevention of disorder or crime, for the protection of health or morals, for the protection of the reputation or the rights of others, for preventing the disclosure of information received in confidence, or for maintaining the authority and impartiality of the judiciary.

I bolded aspects which I think Americans would assume are going to be open to abuse. The new Irish blasphemy law is rumored to be motivated by a fear of Muslim violence aimed at those who defame their primitive superstitions (the cowardly Irish atheists know that Western Christians tend to be lax about agitating violently on behalf of their superstitions, so they blasphemed Catholicism, this was an error, see below). Though it isn’t just Muslims who are barbaric, a few years ago Sikhs in Britain rioted over a blasphemous theater production, and the arguments that it isn’t speech if it “hurts feelings” were voiced by them as well. This is a normal human viewpoint, protection of patently offensive speech is probably a cultural aberration. What to Americans seems a universal human right is actually a perverse extremism from the viewpoint of outsiders (though do note that the abolitionists seemed to be perverse extremists in their time, so numbers don’t always predict where history will flow)
One of Eric’s stupid commenters linked to this op-ed, Ann Coulter, Hate Speech, and Free Societies:

This is why Coulter’s speech is not just “free” (i.e. bias-free, objectively sent out into the atmosphere). The effects of her speech when launched into public space are not simply situational. They are another series of burps in the historical and currently existing framework that has normalized a particular way of thinking about Muslims, gays and lesbians, and other marginalized groups.

Pretty funny that Muslims are marginalized along with homosexuals, since when Muslims are a majority they have a tendency to persecute or kill homosexuals with more efficacy than other cultures (though not homosexual behavior). Naturally Muslims in the West are exempt from the injunction toward not engaging in homophobia, as it’s naturally part of their barbaric set of beliefs. The op-ed continues:

From this framework, we can see how free speech is a slippery problem. Ironically, it seems to surface when there is a need to stifle speech that challenges social power (which is what the U of Ottawa students were doing – challenging the inequitable social power relations that Coulter’s “speech” upheld).

Really someone should ban the usage of quotations, because morons like this will get drunk on them. Though seriously, I’m expressing a very cultural biased viewpoint here, an American one, and I’m of conscious of this. I really don’t see a point in castigating Canadians for being Canadians, they’re not China or Syria, but neither are they the United States. Even the British have insane libel laws which stifle speech operationally, though there’s a chance that the law might be tightened up. We alone should be the City upon a Hill where the blasphemers and peddlers of bigotry can take refuge, because we’re already the last best and only hope.
* I use the term “barbaric” to refer to societies which I feel express values which are fundamentally different from those of my own so that there is a lack of commensurability of discourse. From the perspective of many Muslim societies American culture is barbaric and kuffar, while the Chinese have their own set of values as evident with the recent conflict with Google over censorship. I use the term “savage” to delineate those societies which dehumanize other cultures. So the Aztecs were savage because they waged wars against other polities for the sake of harvesting sacrificial victims, who were later cannibalized.

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia:

With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined…the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans….

The tree gets bushier? Just see John Hawks and Carl Zimmer.

Check it out, Wiring the Brain.