New PLOS paper, Geographic Patterns of Genome Admixture in Latin American Mestizos. Nothing new, but pushing the ball forward….

A = autosomal
X = X chromosomal

How a Film Triggered a Global Panic:

But Balkenende is only doing what he believes is the best thing to do under the circumstances. Meanwhile, both the secretary general of NATO and Iran’s deputy foreign minister have offered the Dutch advice on how to neutralize Wilders: by invoking Article 29 of the 1948 Universal Declaration of Human Rights.
According to Article 29, individual rights must be limited when it comes to respect for the freedoms of others and where the public order makes this necessary. Ironically, the man who invoked this article is the deputy foreign minister of a country, Iran, where homosexuals are publicly hanged and adulteresses are stoned to death, and when this happens, no one there invokes the Universal Declaration of Human Rights. The Iranian ambassador to the Netherlands also told a group of journalists that freedom of speech is “not unlimited.”
When asked whether the Netherlands could expect a boycott on Dutch products if the Wilders film is shown, the ambassador was evasive but clear. “All options are on the table,” he said. “No one can say what will happen.”
Hans Gert Pöttering, the president of the European Parliament, issued a similar statement. He called upon the media to impose a “code of behavior” on itself and not to publish anything that could be perceived as “derogatory” by members of religious groups. He also warned the Dutch not to “make a contribution to violence because of our freedom.” These clear words of appeasement, which the chief EU parliamentarian directed against the victims and not the perpetrators of violence, urging the former to be on their best behavior, were — as the Frankfurter Allgemeine Zeitung wrote — the result of “anticipated fear” and sounded “dangerously like self-censorship.”

Let’s get real here. It isn’t just any religious gorup; it is a religious group which has produced a militant wing intent on rolling back the Enlightenment’s victories for the right to blasphemy their One True God at the edge of the scimitar. Christian fundamentalists are problematic for a host of reasons, but the central tendency of modern Islam is shockingly illiberal, and I believe that mass media and modern information technology is resulting in less assimilation of Muslims to liberal norms than would otherwise be the case. Those norms include the right to blaspheme without fearing life & limb, a normal fear for most of human history when it came to dissenters against the dominant supernatural paradigm of a given society.
Above you see an image of the head of a pig with a book in its mouth. That is all.
Related: Is your mother a slut?.

Normally I don’t blog politics since I don’t know shit really. I generally subscribe to 2-3 political feeds which I regularly rotate to keep me “hooked in.” Today I saw something so so shockingly stupid, or, brazenly mendacious, that I had to take note. Red Massachusetts?:

…And a Scots-Irish war veteran as the Republican nominee complicates predictions about whom Kennedy Country will support come November.

Most of the commentary seems fine, if disputable; I might not agree, but it’s political pundrity, about as rooted in reality as sports predictions. James Kirchick graduated from Yale with a degrees in history and political science, so I assume he knows something and has the processing power to engage in a fair amount of rigorous ratiocination. The reference to “Kennedey Country” has to do with the fact that Massachusetts is demographically dominated by Irish Americans and their political culture. This is not identical to Scots-Irish, who are customarility Presbyterian. Additionally, in the southern highlands some of the Scots-Irish regions were often redoubts of Unionist-Republican sentiment during the long Democratic hegemony (ergo, the creation of West Virigina). Nor are these two groups similarly distributed across the nation.

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If you are a male, and someone says your mother is a slut, how do you respond? I think most non-autistic individuals, even if they are reflexive pussies as many civilized American men raised in urban areas and suburbs tend to be, will feel an urge to react violently. I think we can agree that someone calling your mother a slut does not have obvious material consequences; it isn’t inimical to your economic interests, especially if the exchange occurs in a bar and your interlocutor and yourself are drunk. I won’t rehash evolutionary psychological arguments for why there’s a tendency for most males to react viscerally with rage when someone insults the sexual character of their mother; I simply want to use it to illustrate the power of words and concepts which have no material consequence, and might not even be rooted in fact. A stranger who throws this insult at you usually doesn’t even believe in its accuracy, his usage of the phrase is calculated to offend and elicit a reaction. There are certain things which are sacred, certain lines you don’t cross. Sometimes these are strongly biased by biological parameters (e.g., I suspect near-family incest taboos is one of these), and sometimes they are not. It is the latter case I was thinking about a few months ago when I read Rome & Jerusalem: A Clash of Ancient Civilizations and God’s Rule – Government and Islam.

You see, the ancient Romans and Muslims did not have kings. Kings were tyrants, and the early Roman and Islamic polities rejected such tyranny on principle. So of course, instead of kings, the Roman Empire was headed by an emperor, while the Muslims had caliphs.1 Get it? When Augustus defeated Mark Antony and Cleopatra the official narrative was that the doughty republican traditions of Rome had bested once more the oriental despotism of the Hellenistic world, with their Greek kings and queens. Similarly, the righteous Abbasids overthrew the despotic Arab Kingdom, the Umayyads. In its place they established a genuine Islamic state which was guided by the traditions of the community as opposed to profane naked autocracy. Right….

As you can see here, the extent of the self-deception and semantic delusion is really humorous. Now, it is true that the early emperors of Rome tended to keep up the illusion that they were simply stewards of the Roman Republic with some verisimilitude.2 Augustus’ shtick was that his was a restorationist project; he was no dictator or king, just the First Citizen. Similarly, the early Abbasids were ostensibly bringing the vision of the Islamic community to its true fulfillment (especially the Shia party), whereas the Umayyads had been worldly Arab tribalists more in keeping with the values of the jahiliya. But the reality is that Augustus’ Rome was as republican as Constantinople in 1453 was the capital of the Roman Empire. Similarly, the Abbasids resurrected the values of the primitive ummah by way of formulating a more ideologically coherent oriental despotism than the barracks state of the Umayyads. Despite their more effective propaganda the Abbasid caliphs integrated pre-Islamic Sassanid motifs into their court far more than the Umayyads ever had.

But this sort of pro forma packaging mattered a great deal. Muslim soldiers were enraged and shocked when the conqueror of Spain allowed his Visigothic wife to convince him to don a crown and so indicate kingship; they accused him of becoming a Christian. This despite their own fealty to an Umayyad regime which was excoriated later in history by mainstream Muslims as a semi-pagan autocracy! These sorts of issues tie in to events and dynamics we see in the modern world. Muslims, for example, wish to criminalize blasphemous criticism of their prophet, desecration of their holy bookm and disrespect of their religion generally. Obviously they’re met with skepticism from non-Muslims, but a number of them analogize their position to that of Europeans who ban Holocaust Denial. Dismissing the details of the analogy and my personal rejection of these Holocaust Denial laws, it is important to state that I think it trivializes the extermination of millions of human men, women and children on an industrial scale to compare this to an insult to an idea, or the desecration of a configuration of ink, paper and binding which results in a Koran. My own perspective is pretty obviously conditioned by the fact that I accept that human beings were tortured and killed en masse 60-70 years ago, while I don’t think that the Muslim religion is anything more than a belief system rooted in made up stuff. The only damage is done to feelings, not a One True God. That being said, a billion people have invested a lot of psychological import into these beliefs and they just go insane when you insult those beliefs. Billions of others can empathize on so
me level because they have other beliefs which are cognate in the broad outlines.

In the West, what I like to think of as the civilized world, there has emerged a consensus that constrains, and almost devalues, sacred lines and the right to take offense. Feelings rooted in immaterial beliefs still matter; if one makes a religious objection to a public norm one is accorded more credibility than if one makes an areligious objection (e.g., prisoners who need a special diet due to religious restrictions vs. those who really hate the taste of the cuisine). But to a large extent the power of religion to defend itself from blasphemy through the arm of state power has been abolished, even if there are blasphemy laws on the books in many jurisdictions. The transgressive assertions of men such as Denis Diderot in the 18th century broke down those barriers, and the reality of religious pluralism in the United States meant that reciprocal blasphemies between Protestants and Catholics occurred which did not elicit the intervention of the state as in the past lest it enflame the conflict furthermore.

In any case, the attempt by Muslims to resurrect in the West the enforcement of pietas by governmental fiat has changed my own opinion as an atheist about the value of religious pluralism. Because I believe that religious sentiment and feeling is normal, and will be dominant in our species barring a reprogramming of the software, I think that one religious tradition is probably easier to manage in terms of negotiating the terms of relating state, religion and the role of the ontologically blasphemous irreligious minority within a society (by ontologically I mean that by the very nature of my atheism & apostasy I offend against Islam, for example). Since the militant secular party is by definition a negative one, objecting to the prescribed social pieties, it is much simpler when one has to face-off with a unified front and one dimensionality of supernaturalism. With the rise of a polycentric supernatural marketplace the act of negation multiplies in complexity as the permutations of absurdity increase ever upward. Diversity has costs, the common norms are essential so that even transgression of those norms can be regularized and tolerated reasonably.

Addendum: I want to add that I was in rural Bangladesh during the Rushdie Affair. I was called on to translate some photocopies of English pamphlets which in hindsight totally misrepresented the The Satanic Verses (long story short, they made it sound like Muhammad’s wives were starring in a novelization of EuroGangBang #69, and it was kind of awkward for me since I didn’t know the appropriate words in Bengali for a lot of the stuff). But it was notable that many of the young Muslim men were enraged about something that they barely even comprehended in its accurate details. Feelings….

1 – Minor note before David Ross points this out, but the term imperator did not come to be regularly used by the emperors until the Flavians. Before that they had been only the princips.

2 – The transition from First Citizens of the Julio-Claudian period to the autocrats (of the Byzantine Empire was a gradual one. The Flavians in the late 1st century reiterated the hereditary principle and banished any delusion that a senatorial resurrection was in the offing. Septimius Severus in the early 3rd century crystallized the idea that the law was an expression of imperial will as opposed to senatorial consensus. Diocletian in the early 4th century introduced the proto-medieval regalia which typified Byzantine autocrats, an oriental court and diademed crown.

I just purchased a copy of A Biologist’s Guide to Mathematical Modeling in Ecology and Evolution by Sarah P. Otto and Troy Day. My main rationale for getting this book was that I wanted a reference with the kitchen sink included, and, I was curious about mathematical ecology. This text leans a bit more toward ecology than I would have preferred, but it has a lot of good stuff and I’d recommend it if you are curious about the stiff formal side of biology. I liked the fact that there was a section on probability as well as linear algebra; Otto & Day only assume algebra and calculus, so it is totally accessible to undergraduates. It really isn’t that dense in terms math and prose, the type set means that the 700+ pages throws a bit less at you than you might assume. There are a load of illustrations too if pictures are your style.
(I really appreciate the tables of formulas clustered appropriately by category and separated into discrete and continuous sections; nothing new, but nice to have it all on one platter so to speak)

Everyone on ScienceBlogs^TM is talking about Arthur C. Clarke. I put up a short post where I noted his passing. I wasn’t a super fan of Clarke’s fiction, though I found it interesting and thought provoking. My personal favorite was the The City and the Stars, which tells the story of a future human civilization of immortal citizens who have turned away from the cosmos. Clarke, being a science fiction writer, does not depict this inward looking conservatism positively, though to some extent one might posit that it is a sort of Benthamite utopia.
And that is the significance of men like Clarke; they offer up a vision of the future where humanity explores the cosmos. When I was a child I remember seeing a clip of Joseph P. Kennedy II, the son of Bobby Kennedy, making a speech in congress bemoaning funding for NASA which might come at the expense of social programs. I was stuck by the argument the time, and frankly somewhat alarmed. Obviously no one wants to take food out of the mouths of babes, but such an extreme utilitarianism seems spirit sapping to me, pedestrian if you will. Ultimately Kennedy’s argument hinged on exactly what sort of vision we might have for the future and the present; I doubt he personally abdicated the life of aesthetic appreciation because so many are malnourished around the world. How many lived in want so that Joseph Kennedy could live the life of leisure, philanthropy and activism which is the birthright of a Kennedy? The choices we make in our own lives show that though a spare utilitarian moral calculus may be an place from which the discussion can start, it is not the end of the story.

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Read all about it. He was no prose stylist or a crafter of character, but oh the ideas!

John Hawks responds to the new paper in PNAS, Close correspondence between quantitative and molecular-genetic divergence times for Neandertals and modern humans.

I read Christmas: A Candid History walking home last night. It’s a small compact book so walking and reading works well. In any case, there was some surprising information here. The basic outline that Christmas, as we understand it, is in large part a co-opted pagan complex of festivals is there. No surprise. But the author claims that the suppression of St. Nicholas and his festival during the Reformation in northern Europe had the side effect of enabling the resurgence of pagan supernatural folk-heroes! In other words, without St. Nicholas the rural peasantry of German and Scandinavia simply drafted a replacement from their own folk history for their mid-winter celebrations, and that replacement naturally manifested many more pagan elements than St. Nicholas the Christian bishop because it was outside of church control.
But St. Nicholas as Santa Claus remains robust in the United States. Why? Turns out that this figure was a creation of the circle around Washingtin Irving in New York during the early 19th century. New York was of course once a Dutch colony, and many of the elite families still proudly declared such antecedents. Iriving’s circle simply asserted that the festival of Sinter Klaas had once been very prominent in New Amsterdam despite no evidence to support this, and the rest is history….

It’s hard to have a recessive lethal hang around for a long time without some kind of heterozygote advantage: selection reduces its frequency. If the population is even moderately large, more than a few thousand, changes in allele frequency over time are very predictable: deterministic.

That also means that one can calculate past frequencies, as long as as these assumptions hold (i.e. as long as there was no tight bottleneck & selection coefficients were the same).

Going forward in time , the frequency of a recessive lethal with no het advantage declines more and more slowly, since the ratio of homozygotes to heterozygotes declines as the allele frequency declines. But if you go backward in time, the frequency grows, and it grows more and more rapidly as you go further and further back in time. This doesn’t continue indefinitely: the frequency can’t go above 100%. Project the frequency of such a recessive lethal back in time and you hit a singularity.

Today, lethal cystic fibrosis alleles have a frequency of 2% in northern Europeans. Unless I’m wrong, it takes 50 generations for a recessive lethal to go from almost 100% to 2%, and another 50 to go from 2% to 1%, assuming no reproductive compensation. ‘Reproductive compensation’ means that parents have another kid when one dies young and thus end up with the same number of children raised to adulthood. This effect weakens, but does not eliminate, selection against lethal recessives. With full reproductive compensation, it takes 80 generations for a recessive lethal to go from 99.5% to 2%, and another 75 to go from 2% to 1%.

If the frequency of lethal CF alleles is 2% today, there must have either been a selective advantage in heterogygotes over most the of the past two thousand years, or the population of northern Europe must have crashed down to a few hundred or less sometime during that period.

There was no such crash, which would have been worse than a nuclear war. Indeed, there was no bottleneck of any kind in that time period: we know this from the historical record. Events like the Black Death do not a bottleneck make: you need to get the population down into the low thousands or less. The Black Death left tens of millions.

So lethal CF mutants had some kind of selective advantage, or were closely linked to some allele that did.