Recently Ayaan Hirsi Ali has been making the rounds on the talk shows because of a new book. A few weeks ago she was on a Boston radio show, and you can listen to the whole interview, but, I suggest you fast forward to 24:30 and listen to the female Muslim caller. Listen to her voice, the outrage and shock, the tremor because she can’t abide what she hears. I generally listen to a radio feed while I’m at work and Ali has been on a few shows, and this is a common response. Whatever reasoned critiques this variety of caller has of Ali’s assertions (I am, for example, not positively inclined toward Ayaan’s recent tack of repackaging herself as a Muslim by culture), the emotional impact of seeing their religion criticized and verbally raped makes them nearly unhinged. This is not an abnormal reaction, people attach great value to their religious identity, and when it is assaulted, even rhetorically, they take it quite personally. Remember that the persecution of Christians in the Roman Empire was in large part justified by their ‘atheism,’ their public disrespect of the traditional gods not their own. The concept of blasphemy, violation of taboo, is pretty universal. That being said, after the 18th century Christendom, and what became post-Christian Western civilization, shed the taboo against criticizing religion. It is simply part of the freedoms we take for granted. Most of the callers who have reacted with outrage against Ayaan Hirsi Ali are immigrants, and to me it seems quite clear that their outlook has been shaped by the inviolable nature of Islam and Islamic ideals in their societies of origin. When people talk of a “Western Islam,” I think one of the things one must look to as a metric or indicator is acceptance of violation and blasphemy, a disrespect that Christianity has become accustomed to over the past few centuries.

One may contend that provocateurs such as Ayaan and Sam Harris go too far in violating the public pieties, but if you listen closely to what the caller asserts you can see why such a violation is necessary. Her reiteration of the “true Islam” in direct contradiction to the general way Islam is practiced does nothing to establish a common ground, it reflects the dreamland of her own imaginings. Fundamentally, those like myself who are secular but generally disinclined toward engaging in an anti-religious jihad because we see neither the point or the possibility of a final victory are skeptical of the hope of a modus vivendi when the delusion extends from down on high toward the mundane world of facts on the ground. Believe what you will of the divine, but accept the reality of the profane and do not fib like a child because you wish it to be so. Your parents may tell you that you are the most beautiful and smartest child of them all, but once you enter preschool you start seeing that there is more to the world than you could ever have imagined. So let’s hope that preschool is in session, inshallah.

See another sign here, and consider making your own here

For those of you who don’t know, check out Allabout-SP.net/, which has an archive of all the South Park episodes. I don’t own a TV mostly because most of the stuff is crap but still compulsively addictive…but the great thing about South Park is that I enjoy 80-90% of the episodes, so there is a good chance that I won’t waste my time.

Nature Biotechnology has a little news article profiling some of the companies driving the cost of sequencing down. There’s ambition in spades:

Companies have also started to win bids under the NHGRI $1,000 genome program. Unlike the $100,000 technologies, which focus on refining and improving existing methods, the conception of a $1,000 genome requires an entirely different paradigm-a discontinuous innovation. Helicos’ technology, unlike the cluster-based approaches of 454, Agencourt and Solexa, could provide such a leap: in the first commercial award under the $1,000 program, it received, in October 2006, a $2 million grant to further develop its single-molecule approach.

According to Steve Lombardi, senior vice president of Marketing at Helicos, “If you had perfect chemistry, and each step was 99.99%, the instrument would generate 100 billion bases a day. The instrument is being designed for that throughput, but the first-generation chemistry will have a smaller yield-around 600 megabases per day.” Improvements in chemistry could move Helicos to the $1,000 genome “in the first few years,” he claims-well ahead of the NHGRI goal of 2014.

Everyone talks about personalized medicine and whatnot, but my first reaction is: wow, are microarrays already almost obsolete? With 600 megabases per day (the human genome is 3300 megabases), SAGE on a huge scale is possible…

Ever since the presence of fetal DNA in maternal plasma was demonstrated a decade ago, a number of teams have been searching for the best way to put this information into practice, so far with fairly disappointing results. The problem, of course, is that maternal DNA is also present in maternal plasma, and given that half a child’s DNA comes from the mother, it’s rather difficult to distinguish the two. The easiest applications, then, are when there is some DNA in the fetus that simply cannot be maternal–a Y chromosome, for example. Sex testing via this method should be rather trivial, though perhaps not that useful (the classic “look at the ultrasound and see if there’s a penis” method also proves rather reliable).

After sex determination, testing for aneuploidies like Down’s syndrome should be next lowest hanging fruit. Currently, the levels of a number of proteins are tested in expecting mothers, and those who have levels at the extremes of the distributions are advised to undergo amniocentesis to confirm or negate the results (the best tests now have a detection rate of about 80% and a 7% false positive rate, which, while not awful, certainly isn’t diagnostic). As amniocentesis carries a non-negligible risk of causing a miscarriage, it would be desirable to get better results non-invasively.

Two new papers attack this problem from different angles–one uses paternal information to find SNPs that distingush maternal from fetal DNA, and the other cleverly uses levels of RNA from a gene expressed only in the placenta. Neither is going to replace amniocentesis just yet, but technology marches on…

Eventually, will it be possible to get an entire fetal genotype non-invasively? It’s certainly possible, and this could have major implications for “neo-eugenic” practices. Currently, if a couple concieves a child naturally (no IVF), there are only a limited number of genetic tests it’s worthwhile to do, as methods for obtaining the fetus’s genetic information carry the potential cost of killing it. Once that cost is gone and our knowledge of genetics progresses a bit, parents could theoretically “screen” their children for whatever trait they desire without passing through the rather unromantic (and expensive) IVF step. Will many parents abort a child because they don’t like its eye color? Doubtful, but some small percentage will choose to terminate pregnancies for reasons that seem rather cold-hearted.

A few months ago a friend made an offhand comment about how they were on the side of the “Andalusian model.” His assumption was that Al-Andalus, Muslim Spain, was far superior in its method of dealing with religious pluralism than Christian Spain. I’ve read a fair amount of popular & scholarly work on this period and region, and the reality is more complex than the hype. The friend holds a Ph.D. in a social science from Harvard and has a position as an assistant professor at a moderately elite university. He isn’t an uintelligent individual. I tried to communicate to him a few general points:

1) Religious pluralism was a reality in both Christian and Muslim Spain

2) Subordination at the expense of the religion promoted by the the elite was the norm throughout this period

3) Persecution of Jews occurred both in Muslim & Christian Spain

4) One can see a general trend where the dominant religion, whether it be Christianity or Islam, tends to become less tolerant when its numbers are great enough to dispense with accommodation with the majority (or what has become a minority)

The issue that I had was that my friend was making an identity between Muslim Spain and the post-Enlightenment West in regards to freedom of religion when that freedom did not exist in the former. Al-Andalus’ tolerance only exists on a relative scale in comparison to the later Spanish expulsion of Jews, Morsicos (crypto-Muslims) and persecution of religious nonconformists (Protestants). The expulsion of Jews from Spain looms large in our minds because of its recency (and its memory in the Sephardic Diaspora), but the pogroms in Muslim Spain during the 10th or 12th centuries were nothing to sneeze at. Similarly, Jews and Muslims played roles in the life of Christian states throughout the transitionary period from 1000 to 1500 (e.g., Muslim soldiers were employed by Christian kings). It would not be factually incorrect to romanticize some of the medieval Spanish kindgoms set against the oppressive nature of the Spanish monarchy after 1492.

There are two major issues that loom in the background for me. First, was Al-Andalus more tolerant than Christian Spain? Let’s say we evaluate the period between 700 and 1800. If you construct a “persecution” index with a host of parameters (e.g., expectation someone is subject to a pogrom in any give year, etc.) I would probably bet on Al-Andalus. That is, integrating over the time from conquest to reconquest religious minorities might have had a better time of it in Muslim Spain than Christian Spain from 700 to 1800. That being said, the difference is quantitative, not qualitative. Second, one needs to put the contextual issues on the table. Muslims were a small minority in their domains for the first few centuries of Al-Andalus, so it was simply not practically feasible to engage in excessive religious persecution. Similarly, afer the Visigothic monarchy converted to Catholic Christianity from the Arian sect in the 6th century there seems to have been more persecution of Jews. Why? Was Catholicism fundamentally more anti-Semitic than Arianism? I suspect not, rather, the Visigothic elite before their conversion were a religious minority, and as such they were in no position to use the ideology of religious conformity to support their rule since they themselves were at variance with the majority confession. After their conversion to Catholicism they had nothing to lose, and everything to gain, by engaging in religious intolerance as it solidified their rule and identification with the religious majority whom they had so recently joined. Similarly, the Catholic rulers of the Iberian peninsula did not become any less tolerant over the five centuries of the reconquest, the demographic balance of power shifted from Muslims to Christians (just as Christians had once converted to Islam, so Muslims who lived under Christian rule slowly converted over time to Christianity).1 What people tend to do with cultures in a historical context is similar to what they do with individuals in regards to the Fundamental Attribution Error. Instead of Muslim or Christian tolerance & intolerance emerging out of the situation, they become reduced to cultural essences. My friend had internalized and essence of Muslim Spanish culture that it was “tolerant” as a matter of principle when in reality it seems more a matter of pragmatism. The reconquista states also engaged in this pragmatism for centuries before the expulsions and forced conversions began. Conversely, during times of chaos and stress, and when Muslims had attained numerical dominance, Jews and Christians also were on the receiving end of Islamic persecution.

Which brings me to my final point: attitudes and sentiments about Muslim Spain are not about history or an analysis of the data, they are about the beliefs we hold about the modern world in regards to the values we deem to be precious. That is, my friend, scholar though he is, was not really interested in the nature of life in medieval Spain, he was making a comment about his adherence to the principle of religious toleration and the separation of church & state. Muslim Spain is simply a notional marker, a signal, the historical details are pretty much irrelevant, it is the legend that matters. I bring my friend’s educational qualifications up because this is a person who is intellectual in orientation, but in hindsight I realize that bringing up the minutiae of historical detail is pointless, and fundamentally a distraction for him. The history is grist for the mill of ideology, not a thing in and of itself. An analogy might be the Bible, no matter the reality of the scholarship Christians will extract from the text and historical details points of relevance to them and their daily lives. Similarly, conservatives and liberals will take from the life of Thomas Jefferson the slices which are relevant to them, no matter the reality of the sum total of his beliefs and sentiments.

This does not mean we can not glean reality from the past, and understand how it was. Rather, I am implying that for most humans such scholarly points of detail are not important, the past is a fiction which simply allows them to justify their own ideals with a more ancient patina. Of course, on this blog I do insist upon fidelity to reality as we understand it. It is simply an acknowledgement of reality and its power than I concede that historical accuracy is of little concern to most, and so it shall ever be.

1 – The Moriscos expelled in 1600 were crypto-Muslims who could not be assimilated into the Spanish state because of the nominal nature of their Catholicism. But, that does not mean that all Muslims living under Spanish rule were destined to become Moriscos, rather, it seems likely that the great majority converted, just as many Jews became Catholics.

Over at my other blog I have three posts on Etruscans. Dienekes has been covering the topic closely as expected. The key here is that genetics seems to have answered the age old question of where the Etruscan people, one of the most important influences upon ancient Rome, came from. The Etruscans seem to have spoken a non-Indo-European language and emerged rather mysteriously during the early first millenium BCE to dominate the northwest coast of Italy (roughly, modern day Tuscany). Herodotus transmitted the legend that the Etruscans were originally from Lydia (roughly, western Anatolia), but the “Father of Lies” lacks a certain rock hard credibility. Understandably, contemporary scholars were skeptical of this exogenous origin, and the dominant tradition during the late 20th century among archeologists and historians was that folk movements were of minimal demographic impact. A less exciting, but more plausible, explanation seemed to be that the Etruscans were an indigenous cultural tradition influenced by the spread of Greek and Phoenician civilization to the western Mediterranean. But in this case, the sexy answer was the right one. I’m generally persuaded by Henry Harpending’s contention that reading “neutral” markers has an aspect of tea leaf interpretation, but this is far more applicable to grand narratives which are global in scope. Genetics does not lend itself to answering all questions, in particular due to the genetic exchange between neighboring populations equilibrating allele frequencies over the generations, but in this case the long distance migration of a whole people in an alien genetic landscape left a discernable impact down to the modern day.

Success begets succes, Dienekes was looking closely at genetic data due to the publication two papers which suggest an Anatolian origin for Etruscans (there has been previous mtDNA going back at least 5 years as well). He finds that central Italy exhibits a relatively high frequency of a variant of Haplogroup J, famously connected to the spread of farmers from Anatolia into Europe during the Neolithic revolution. Not that we’re on the trail of the definitive answer I suspect that things will “fit into place” far more easily. Scholarship is informed by scholarship, knowing that the Etruscans are of Anatolian origin, at least partially (remember that the presence of mtDNA suggests that they brought some of their women folk over) a massive movement.

Do you remember the age before polling in politics? I don’t. Today we bemoan the emphasis on polls and idealize the past, before candidates knew in scientific and statistically significant detail the temperature of the democratic water. But no one is going to ban polls in the near future, for every person who complains about survey data there are hundreds who are clicking refresh over & over to find the most recent tracking results on their website of choice.
I think something similar is necessary for the sciences (or scholarship in general). Is George Lakoff a laughing stock (as Chris would have us believe), or a thinker of gigantic Aristotelian proportions? I suppose if you were a cognitive scientist you’d know, your sample of individuals in the field with whom you’d engaged in personal communication would be vast and you could get a sense of the direction that the wind was blowing. But for someone outside the field you basically have to trust someone on the inside and hope they aren’t misleading you (or, themselves). Is multi-level selection the next big thing in evolutionary biology, as Bora claims, or is it a relatively marginal and muddled field, my own general perception? Bora has made the Kuhnian claim that multi-level selection’s day will come when the older scientists die off, but how do we know that his perception is correct? One’s own sample is obviously going to be biased toward those with whom one is on common ground with, perhaps there are enormous social science departments steeped in conceptual metaphor theory that Chris as no knowledge of because he is boxed within his old fashioned world of symbolicists?
I think my point is pretty clear here: in the sciences quite often lay persons are in the position where they know with great confidence that a theory is absolutey accepted at its level of precision (e.g., Newtonian Mechanics) or totally rejected (e.g., the Aether theories). It is as if our knowledge of allele frequencies was certain with any degree of confidence only if they were operationally fixed (i.e., greater than 99%) or very rare or non-existent (i.e., less than 1%). Not only would my proposal help the public, I think it could give scientists some perspective about their position within their discipline.

The Leutgebs and the Mosers have brought us another interesting datapoint regarding how the hippocampus segregates or lumps the representation of spatial environmens. They recorded from the CA3 and dentate gyrus subregions of the hippocampus while they moved rats between a series of ‘morphed’ environments, moving gradually from a circular to a square arena. The idea is that CA3 tends to lump representations while DG tends to split them apart. No time to chat right now, but here’s an excerpt from the commentary by Andre Fenton:

The authors confirm that CA3 place cells respond to small deviations in the spatial environment by lumping. In other words, the same neuronal discharge patterns were observed in CA3 regardless of whether the rat was in a morphed or unmorphed circular or square box. Larger deviations from either environment caused rate remapping in CA3. The dentate gyrus was quite different. Single dentate granule cells had more firing fields than did individual CA3 cells. Granule cells responded to small morph deviations in the rat’s environment by changing both firing rates and firing fields unpredictably. Thus, the dentate gyrus proves a consummate information splitter and the CA3 more of a lumper (see the figure). Small changes in spatial input information caused large changes in dentate gyrus output to CA3 but virtually no changes in CA3 output to CA1.

I had a dream last night that I was at a seminar where Stefan Leutgeb was explaining these findings and Edvard Moser was in the audience and began correcting Leutgeb and they got into an argument but started speaking in French. Miraculously in my dream I could understand French and was able to impress the student next to me by explaining the argument. I don’t remember what they were arguing about though. Too-da-loo.