Did you like the video of the Dancing Air Force Cadet? If so then you'll probably also like these two dudes singing to the Backstreet Boys. Pay attention to the guy in the background who seems completely oblivious to the goings on. These guys sure know how to emote. Maybe when they take their act on the road, they can talk to the Air Force dude and get him to Federline on stage for them.

Update from Razib: While we're at it on videos, check out the Guinness evolution commercial if you haven't. And yes, those are icthyosaurs.

Update from TangoMan: Here's Yoda doing HipHop for some StormTroopers. Here's Anoop Dog doing Drop it Like a FOB. Here's the Two Chinese Dudes doing As Long As You Love Me and here they are doing 3 different Chinese songs and notice the one guy's eyes, what's up with that, then notice that the background guy is part of the act when he participates at the end of part 1, and here they are singing Radio In My Head with some acting thrown in towards the end.

There are omnipresent nods to the "Cult of Diversity" in the mainstream culture. This is no longer a powerful faction, it is now an essential face of the State Cult as well as the Elite Cult. But what exactly is diversity??? How do you precisely describe it?

One way to do it is simply transpose into sociological discourse the usages of information theory common in ecology. For example, the index of species diversity:

In this case, s = number of species p_i = proportion of total sample belonging to ith species.

The maximum diversity you can attain is obviously:

In other words, every individual within the population is of a different species.

The "evenness" or "equitability" of the population is given by:


The relevance to discussions of "diversity" is obviously that H' and J' are related, but they are not equivalent. In verbal terms, there are different ways one can attain a state of diversity. How relevant it is to your perception of aspects of public policy are dependent on your values and your goals. For example, in regards to immigration, the record of writings and opinions expressed on this weblog by me over the past 3 years suggest that I favor 1) a relatively non-diverse stream of immigrants in terms of educational qualifications (they should be above the population median), 2) but diverse in terms of national origin (so that group mobilization of non-natives is dampened). I also of course prefer that the stream is moderate enough that the rate of absorption is in equilibrium with the rate of immigration. Now, in everyday discourse "diversity" is clearly sometimes highly sensitive to the states of "s," that is, an Asian is not interchangeable with a Latino is not interchangeable with a black (see How Asians became White by Imbler Volokh). On the other hand not all dimensions have equal weighting. Who talks about the "diversity" that working class people of all races bring to a firm, as opposed to specific racial minorities (be they privileged by class or not)?

Those of us who dissent from the Cult of Diversity are at a sharp disadvantage at the current juncture. Nevertheless, the guerrilla strikes must continue until the day someone runs into the marketplace and declares that God is dead. At that point, we will be ready to offer an alternative, and more ancient, vision. But there will also be others, ready to offer a tried and true formula. Remember, the Cult is simply metastable.

Addendum: Let me be specific as to why I posted this, I really tire of the abstract, idealized and mysterious moving targets of "diversity." I recently read a Guardian piece about 49 Up. I've watched all the previous episodes of this series, and plan to watch this one in the near future, but the columnist states: "There is only one black participant and only four of the 12 are women." First, the participant is of mixed-race. Second, fact, the UK is 92% white in 2001. 1 out of 12 is about an 8% representation on the show, about right. But since the show selected its participants in the 1960s, one should more properly judge the representation by the proportions in those days. The overall point is that like the commonly accepted claims of Mystery Religions even the most superficially ludicrous contentions of the Cult of Diversity get a pass. This is because True Diversity is not something that exists in this world, it exists in the Other World, the Kingdom of Heaven. The numbers really don't matter from what I can tell because those who promote diversity most strenuously seem to see numbers as means, not ends (else why not more concern about the declining proportion of males receiving bachelor's degrees?). In the near future I'll offer what I think appropriate (acceptable) H' and J' values for the USofA are, with stipulations about the character of species diversity (so to speak).

As the title says....

A few weeks ago I finished reading 1491 by Charles C. Mann, which I haven't said much about because it didn't tell me much new (i.e., there were many more natives than we had earlier thought, the Clovis culture wasn't here first, Amazonia shows strong evidence of being an anthropogenically shaped environment). I might comment in detail at some point, I have a book on Maya history that I want to read at some point that might give me some ideas that are bloggable, but, I want to highlight a passage in the book where the author talks to a geneticist in regards to native susceptibility to Old World pathogens:

...I again telephoned Francis Black. Being genetically determined, Indian HLA homogeneity cannot be changed (except by intermarriage with non-Indians). Did that mean that the epidemics were unavoidable...Could the mass death have been averted?

"There have been lots of cases where individual towns kept out epidemics...."

He stopped speaking for long enough that I asked him if he was still on the line.

"I'm trying to imagine how you would do it...."
...
"You'd have to have the entire hemisphere doing that. And the Europeans would presumably have to cooperate, or most of them, anyway. I can't imagine that happening, actually. Any of it."

As I have noted many times before, the HLA loci, which are crucial to our adaptive immune system, are undisputed cases where genetic diversity has been crucial to long term fitness. Some of the HLA alleles coalesce before the chimp-human speciation event, you might share some alleles with chimpanzees, but not with your own siblings! If a mutation is neutral, its chance of fixation is 1/2N_e, where N_e is the effective breeding population. In other words, the larger the population the less likely that a mutation is likely to random walk in frequency until fixation, but given enough time, there will always be turnover. If the mutation is favorable the probability of fixation is 2s, where s is the selection coefficient which defines the fitness advantage confered by the derived allele against the population mean fitness. Again, given enough time one imagines that one favored allele should fix itself within a breeding population. The deep time persistence of numerous alleles on these loci in most world populations suggest either heterozygote advantage or frequency dependent selection (where lower frequency would increase fitness).

Most of you probably know why this is relevant for native peoples of the New World: they exhibit relatively little HLA diversity, and, the frequencies of their modal alleles are often rather high. There might be many reasons for this, not least of which was the likely population bottleneck most of their ancestors went through. Additionally, Mann reports that some researchers are finding that the helper-T cells of native peoples seems to be biased toward resisting parasites, rather than against microorganisms, as is the case amongst Europeans (one reason might be the relative lack of domesticated animals to incubated species jumping pathogens).

This isn't particularly new information, and normally I wouldn't repeat it, but do for two reasons. First, a few weeks ago an acquaintance of mine expressed skepticism that populational level genetic differences could have any relevance for the human sciences. In this case, the arc of world history was crucially affected. But the second point is that the highbound population figures for the New World implies that within 200 years between 1500-1700 the human population on this planet might have declined by as much as 20%. We are generally aware that rabbits were an invasive species which swarmed across a vulnerable ecosystem in Australia, or flightless birds were doomed to extinction in the face of rats and cats. And yet I had never paused and reflected that evaluated on the species level the short term impact of the contact between the Old World and New was so devastating for our numbers! Granted, I am personally skeptical of the highbound numbers (on the order of 100 million) given as a population base for the New World, but even more conservative numbers are sobering (the 2-4 million range seems highly implausible to me).

It is a sobering reminder that reality does not brook our moral sensibilities, and I can't but help chuckle at some of the more benign renderings of the Strong Anthropic Principle.

Related: Here is a precis of Mann's book in The Atlantic.

John Emerson has a post titled The College of My Dreams up. He describes his program as a "reactionary leftist" category, and stipulates that 'actual science and math work, not just "History and Philosophy of Science"' would be demanded from students at this institution, which would nevertheless specialize in the humanities. I have many friends who have humanities backgrounds who deeply regret that they took "astronomy 101," rather than a real introductory level chemistry course. Too often science courses geared towards humanities majors emphasize the facts of science rather than its technique, in other words, ass-backwards. But back at John, I would state that I also think that science graduates should have to complete some sort of University of Chicago-lite (i.e., the common core) sequence which introduces them to a lexicon that allows them to more fully participate in the public life of a republic. The vast majority of individuals with science degrees (i.e., 99%) will not live in a world of academic science for science's sake, they will be citizens for whom their science background gives them a grounding in their profession or career, but the ends of their life will be more prosaically human.

Of course, all this is fairyland dreaming because the flat-out fact is that college students are getting dumber and dumber. This isn't because Americans as a whole are dumber, just that more Americans are going to college, and pretty soon you'll start sampling the genius of the 1 out of 5 Americans who believe that the sun revolves around the earth.

CSPAN's Booknotes has an archive site. You can read transcripts or watch videos. Good if you are doing something on the computer.

A few weeks ago, one Randall Parker forwarded me this article, Historian challenges assumptions about religious conflicts, which claimed to "debunk" the "clash of civilizations" narrative. Brian Catlos asserts:

"Where my research and data leads, though not intentionally, is to debunk the notion of a conflict of civilizations--a conflict between groups of people who identify themselves as Christians, Jews, or Muslims and who articulate their struggle as a result of ideology and national identity," said Catlos. "Rather what's really behind history and contemporary human affairs is the interest of relatively small groups who often interact without regard to ideologies, national, or religious boundaries."

Catlos' contention is frought with ambiguity. What does "often" mean? Just because people can't "articulate" doesn't mean there isn't something substantive underneath the cognitive surface. But my interest was piqued, so I decided to get Catlos' book, The Victors and the Vanquished : Christians and Muslims of Catalonia and Aragon, 1050-1300, which was an elaboration on his Ph.D. dissertation. I had already read a fair amount about the mudejars, the indigenous Muslims of the pre-conquest unified monarchy states before the fall of Granada in 1492, in Infidels: A History of the Conflict Between Christendom and Islam. In this book Andrew Wheatcraft spends several chapters surveying the history of Muslims in Al-Andalus, and later Spain, until their final expulsion in 1610. After finishing Catlos' book I decided to check out some chapters of Crusade and Colonisation: Muslims, Christians and Jews in Medieval Aragon, to get a different perspective on the issues and possibly scry any glaring biases in The Victors and the Vanquished. After this minimal reading program was completed I was considering writing up a blog post on the issues mooted and ideas I formulated in response to them, but I thought that it would be prudent to reread Clash of Civilizations and the Remaking of the World Order by Samuel Huntington, as Catlos' contention seemed to be in response to the null hypothesis elaborated in this book a decade ago. I did read Huntington's book when it came out...but I thought a refresh was timely, especially in light of changes in the order of the world since 9-11, and my own personal exploration of cognitive science over the past 3 years might give me a different perspective on the arguments in Huntington's book. I stipulate here a priori the books I've read because they have obviously shaped my opinions and conclusions, and if you take objection to any of my contentions, I invite you to read the books above, or at minimum perform a google print search to get the gist of their theses. My overall conclusion, which I will state beforehand, is that Catlos has debunked Huntington as much as Bohr has debunked Newton, that is, they both explore the same fundamental subject, but on radically different scales of organization. The problem with the analogy above is that history and political science are in no way, shape or form, like physics, so take it for what it's worth.


Let me first mount a minor defense of Huntington. Since the publication of his last book, Who are We: The Challenges to America's National Identity, he has come in for some harsh treatment (there were few blogs when Clash of Civilizations was published). Matthew Yglesias deconstructed and debunked many of the "facts" which Huntington used to make his case against Mexican immigration into the United States, and he's not the only one who made a sport of this game of falsify-Huntington. I remember reading Clash of Civilizations back in 1997 and being a bit irritated when glaring and obvious factual errors popped out at me. For example, Huntington makes repeated references to Ethiopia, but on page 137 he states, "largely Christian Ethiopia and overwhelmingly Muslim Eritrea separated from each other in 1993." Follow the links in the previous sentence and you will see that both nations are about evenly split between Muslims and Christians, with Eritrea possessing a slight Christian majority and Ethiopia a plural majority of Muslims! I knew that then, I know that now, and that's not the only error that is embedded in the book. There are similar problems in Who are We (I read that too). But as you might guess, I still think Huntington has important things to say, and that the models he proposes have value. Let me illustrate my basic stance with some quotations from Defenders of the Truth: the Sociobiology Debate:

...the British 'sociobiologists' did not want to be called that at all. They would have preferred to be called behavioral ecologists, or functional ethologists-anything but 'sociobiologists.' But in his review, Dawkins decided to take the bull by the horns. He said that 'much as I have always disliked the name, this book finally provokes me to stand up and be counted'.... [a negative review of British anti-sociobiologist Steven Rose's book]
...
[Steve] Jones felt that Gould and Lewontin, although their Spandrels argument might contain some truth, effectively told biologists the following: 'Abandon hope, go home, and become a be liberal-arts graduate.'

These two distinct opinions are in reference to the storm that swirled around E.O. Wilson after the publication of his book Sociobiology: a New Synthesis. It was in many ways a deeply flawed book (most people don't remember it now, but Wilson also forwarded some sketchy group selection models). Nevertheless, it triggered a renaissance in social theory and its intersection with evolutionary biology, and was the most recent common ancestor of many biologistic modes of inquiry in the human sciences, from behavorial ecology to evolutionary psychology. Hell, it even helped inspire P.Z. Myers to become a biologist.

My point is that sometimes thinkers are important not for what they say, but for getting the ball rolling, establishing a common hypothesis of reference and framing the issues of importance. As far as Huntington goes, too many of the critiques of him strike me as reflecting a decision to give up and become liberal-arts majors, so to speak. In other words, they submit to the blandishments of skepticism as an ends rather than a means, and abandon the project of positive model building in favor of deriving is from ought because of its theoretical elegance. My post, True believer revisited...., should clue one into how I feel about that sort of attitude. When nothing is discernable, everything is possible.

Huntington's thesis of civilizations existing as cultural atoms that behave as units seems ludicruous on first blush. And in the details it is almost certainly a weak signal in the noise. But, social phenomena being what they are, extracting any signal is difficult as it is, and no one who rebuts a deterministic set of propositions is acting in good faith because I can't imagine that a serious scholar would present their expectations as having no variance or error in the real world. I did not get that from Clash of Civilizations in 1997, and I don't get that now.

Catlos' examination of the dynamics of Muslims in the kingdom of Aragon between 1200-1400 (roughly) is a clarification of that enormous expanse of noise which swamps out attempts to build predictive models. The rough backstory is simple, between 1000 and 1492 the whole of the Iberian peninsula was reconquered by Christian kingdoms from the Muslim polities, in fits and starts, though by 1250 only the emirate of Granada in the far south remained of Muslim ruled Al-Andalus. Between 1250 and 1492 large populations of Muslims lived under Christian rule as mudejars. In places like Valencia they were the majority of the population for a substantial period of time, and their presence was a reality on the ground until the last unconverted Muslims were expelled from Spain in 1610.¹ In Aragon Muslims were likely not the majority for very long, but they remained a substantial minority in both urban and rural areas for several centuries. Catlos' work focuses in particular on Zaragoza and its hinterlands. It is deep in its sourcing, not only does he assay economic records, legal documents, but, he managed to find quite a bit of correspondence and references which pointed to conflicts and events which might not show up on tax or property concerns. So here are some major points in Catlos' work:

• Muslims preferred to ally themselves with Christian religious orders. Peasants would enter into tacit bondage so that said orders would defend the rights of Muslims against local aggressors, sometimes Christian, sometimes Muslim.
• Muslims also tended to look toward higher nobility and the king to protect them against their Christian socioeconomic peers or near betters.
• Muslims had to compromise basic tenets of their interpretation of sharia to "get along" in Christian society. In other words, a dispute between a Muslim and a Christian would be judged according to the law of the Christian, unless the Christian preferred that Muslim law be used. Muslim judges (qadis) would render verdicts, but it would be up to Christian authorities to enforce their judgements at their pleasure and discretion.
• Many of the same religious prejudices that worked against Jews were also applied to Muslims. Muslim males were discouraged from having sexual relations with Christian females, and Muslims had to give due respect to Christian religious processions or risk being lynched.
• The class divisions that were common in Christian society were mirrored in Muslims. In particular the Muslim community, the aljama, repeatedly entered into conflicts with those Muslims who had received exemptions from tax through royal grace. This privileged class of Muslims did not hesitate to litigate to preserve their tax exemptions, even though this was often to the disadvantage of their coreligionists, who were almost always assessed a higher tax than their Christian neighbors (not only did Muslims have to support their own religious institutions, but they were often forced to tithe toward the Church just as their Christian neighbors were). Sometimes the tax exempt Muslims would be targeted by local Christian officials, in which case they would become entangled in a complex dispute where different interests aligned themselves tactically according to their own interests irrespective of religion (i.e., the king would support the Muslims to defend his right to confer exemptions, any Christian religious orders would attempt to reduce taxation on their overstretched tenants, etc.).
• Elite Muslims generally either fled or converted to Christianity. Sometimes, whole villages would convert to Christianity (one instance is recorded because two women from a converso village were brought before an inquisitor because of charges of heresy).
• Muslims were raised to fight for the king of Aragon. In particular, they were valued as crossbowmen. Though they were used in particular against Christian powers, sometimes they were also used to fight other Muslims. Professional soldiers, up the level of officers, of Muslim origin were fixtures in the retinues of many Christian lords. Unlike Jews, Muslims were perceived to have great martial vigor.
  
• When the Almohads (a Muslim dynasty from North Africa which attained hegemon status vis-a-vi the emirates of southern Spain) ventured north into Christian territory, the king of Aragon and local notables reassured the native Muslims that there would be no confusion between them and the invaders. In other words, there would be no reprisals against Aragonese Muslims for the actions of their co-religionists who were foreign. On the other hand, local Christian bandits and militia levies on occasion raided Muslim villages opportunistically because of their special vulnerability (this was common enough that the king repeatedly instructed Muslims return from their refuges in the hills to take up farming).
• Though of undoubted lesser status vis-a-vi Christians, Muslims seem to have sometimes served on town councils.
• There seem to have been little physical and/or linguistic distinctions between male Christians and Muslims. Muslims could speak the Romance dialect of the region fluently (many of their names were Latinate in form), even if many preserved a form of Arabic at home. Catlos points out that this was one reason that there were statutes that instructed Muslims to always dress differently than Christians. Additionally, the transitory period when there were many Christians who spoke Arabic (Mozarabs) as their first language and Muslims who were fluent in Romance resulted in several assassinations because "passing" was easy for "both sides" in conflicts.
• Muslims tended to form the slave class in Aragon, as enslaving Christians was generally frowned upon, and Jews could not own Christian slaves safely in any case. Some disputes arose over the issue of conversos, as some Christian masters preferred their slaves to remain Muslims so as to facilitate their perpetual bondage.
• Nevertheless, in some cases Muslim peasants were in an advantaged relationship with local nobles in comparison to Christians because feudalism did not apply to them in that they were often under direct rule and jurisdiction of the king, so only the king could discipline them.

Catlos' text makes clear that there are two intersecting salient traits of Christian-Muslim dynamics in Aragon: 1) the communities were corporately organized by their own leaders 2) nevertheless, there were innumerable linkages across and above these communal distinctions. Though Muslims were theoretically to be organized as an aljama, in practice many Muslims evaded its authority by utilizing the non-Muslim legal system as well as royal patronage. This, in the case of notables who explicitly chose to remain Muslim, rather than convert to Christianity and strengthen their hand. No doubt the Muslims who refused to pay their tax because of a privilege granted to their forebears by a Christian potentate justified it to themselves in a fashion that dovetailed with their sincere belief, and in fact, some families persisted for centuries in evading tax or withholding property to pay the past tax debt, but their names suggested they still remained believings Muslims, and so continued to persist in keeping their second class citizenship against their "rational" interest. But the dissent from taxation by some Muslims, in particular, the subset of some means and income, had the long term effect of weakening the community in its status vis-a-vi the Christian majority or even the ascendent Jewish mercantile class. The point Catlos seems to want to make is that it seems that first and foremost Muslims acted in their own interests, before looking to their putative ideologically inferred behaviors. The reality is that ostensibly Muslims should not even have been living under a non-Muslim ruler, but because of their importance as a tax base the Christian king and his nobles specifically made allowances for their retention, and even used Muslims to colonize newly conquered territories.

The "debunking" of the Huntington thesis seems to be that Catlos illustrates the lack of ideological commitment that characterized the Muslims of Christian Spain at any given time. In a rank order of priorities, conventionally intelligible ones would be foremost on the list before any specific injunctions made upon them by their faith. Their motives were variegated, just as were the motives of the Christian religious orders who often collected rents from them, or the king who depended on their famous crossbowmen. Sometimes they certainly were not trusted, and seen as fifth columnists, but other times they were subjects of the same king as their Christian neighbors, and men and women who paid tax and sat on the city council. Muslims had their own law courts, but on occasion they would take their disputes to Christian courts if it was to their advantage. They were a corporate community who were functionally dhimmis in reverse, and yet they often subborned the integrity of their own corporation, the aljama, if it was in their individual or familial interest.

There is nothing controversial in this assertion. Consider this from a column by Rich Lowery, editor of National Review, from a few years back where he offers one reason why he won't run for mayor (selling out):

Shortly after the mayoral speculation began, a woman stopped me in my apartment building to ask if I were going to run. It turned out that she was that rarity, a right-wing Manhattanite. But soon enough she was asking me what I thought of rent control. I tried to dodge, saying I needed to study the issue further. She pressed me, then said she'd never vote for me if I wanted to end rent control since she lived in a rent-controlled apartment....

The voter to be was right-wing, ostensibly in principle against rent control, but the circumstances of her life dictated that she vote against anyone who would raise her personal rent. Principles are extremely important when they cut your way. A true measure of principles, of values, is what you do when they will cost your dearly on a personal level. Rational choice might have serious problems as the be all and end all of social science, but, it does make sense insofar as people do tend to work in their own interest first and foremost when they are capable of conceiving the general lay of the land in terms of costs vs. benefits. It may be advantageous to declare that one would be a pauper under a believing king rather than a prince under an infidel, but rarely is this sort of verbal declaration tested.

One problem that occurs when we attempt to understand why people do what they do is thatthey quite often do not give plausible motivations, but rather manufacture a rationale which makes them seem principled, logical or consistent. Cognitive scientists have shown that it is rather easy to get people to make "choices" by priming them a priori with various "random" inputs. When asked why individuals made the choices they did the reasoning was always sharply at variance with the correlations which popped out of the experiments the researchers had run. Humans are natural fabulists, story tellers and myth makers.

In my own family my paternal grandmother told me the tale of how my great-grandfather, her father, found the light of Islam in the 1920s (when she was a toddler). Years later my mother explained that my great-grandfather had been having difficulties with some of the employees in a small dairy processing factory he owned, and, some of his dairymen in the fields were refusing to produce their quota. The reason was that the part of Bengal he lived in was going through Muslim religious revivals, and some of his workers were using his Hindu religion as a pretext toward organizing their labor to extract higher wages or portions. My mother did not go much into much more detail, and never said anything explicitly, but later it came to my attention that my great-grandfather converted to Islam under sponsorship of my paternal grandfather's father, who was the alam (prayer leader) of the local mosque and the scion of a Muslim family of some reputation. The subsequent marriage of my paternal grandmother to the son of the alam, and the one of the wealthier local Muslim landowners, solidified the entrance of my great-grandfather into Muslim society, and there were no protests any long against "working for a Hindu," since their employer was a Muslim in good standing (any protests based on religious grounds at least were now baseless and indefensible). This story illustrates the social variables which scaffolded the cognitive commitments my great-grandfather made. As the eldest and most successful son in a region that was overwhelmingly Muslim (this was one of the more Muslim areas of Bengal), he had less to lose personally from leaving his established Hindu social networks than if he lived in a Hindu majority area. As it was, there was also a local Muslim establishment which was willing to accept him once marriage ties were solidified. Did my great-grandfather realize this on a conscious level? If he did, I doubt he thought about it in too much depth, rather, the story he told was likely one of spiritual discovery. Nevertheless, most people in the area seem quite aware of the circumstances behind the conversion, as my mother's family comes from a neighboring locality and she was aware of the general circumstances during that period (as told to her by someone who was alive at that time).

I am not a pure materialist, there are other motivations that drive human beings. As I alluded to above, social context matters. A lone Muslim converso risked alienating their natal social networks before they were able to ensconce themselves into a new Christian identity. That explains the fact that there were records of mass conversions of villages to Christianity, in this way an entire social network was simply transferred and individuals distributed the risk amongst themselves (and removed the primary cost, alienation from their neighbors). Additionally, elite individuals with special skills and prominence can also shift between networks, i.e., renowned Jewish rabbis who converted to Christianity or Muslim warlords of some reputation who entered the service of a Christian noble and accepted baptism, ergo, entrance into the respectable Aragonese elite.

But if you asked these people later why they changed religions, their justification is often given in terms of the intrinsic appeal of the new religion. An emphasis on the special character of a belief is I think often fallacious at its root. I recall reading a book once about Jewish-Christian marriages, where Christian wives who had converted to Judaism missed the "Jesus of their youth." One contention that many Christians make is that their religion evokes a personalized aspect via the incarnation that no other faith can compete with. There is perhaps something to this argument, but I think a more likely explanation is that Protestant Christian culture in the United States emphasizes the personal relationship with Jesus, and I would argue that some Jewish, Muslim and Hindu reformist groups are mimicking this pattern using their own motifs (the Catholic Charismatic movement is in some ways a cultural mimicry of a Protestant innovation). The rather detached character of Jewish worship in comparison to Christian worship might have little to do with the religion itself, but rather all to do with the character of those who are doing the worshipping (that is, Episcopalaian services might resemble Reform services more than either resembles Assemblies of God services or Lubavitcher prayer groups).

With all that said, regardless of the "reality" of cognitive identities, shibboleths also matter. There is a wealth of psychological literature (see The Nurture Assumption or Not by Genes Alone) which suggests that even the most arbitrary identities tend to elicit in humans a "groupishness" which induces some level of altruism toward those within your own group. The point is that the character of the identity itself doesn't matter in regards to its eliciting a basal level of identification. If you want an example of an identity which seems rather frivolous, consider sports teams. Republican, Democrat, atheist, Born Agan, etc., Redsocks fans have a bond. Similarly, I recall defending Rush Limbaugh against the criticisms of liberal friends in the early 1990s after I found out he was a Steelers fan (I cared about such things in those days). The cross-linking of various identities results in the inability to generate expectations which are free from a large error because of other confounding factors. An error is almost always so large that any generalization can be easily "debunked."

But in regards to Catlos' and Huntington's theses, the former is focusing on the enormous error generated by the cross-linkages of identity and interest, while the latter is focusing on a few salient dimensions which are signals within that noise. And I think the signal is important to focus on even if there is a great deal of noise. On 9-11 3,000 Americans died in the name of the Muslim God. It is really irrelevant on a substantive (as opposed to politico-rhetorical level) to argue about whether this was justified by Islam, whatever their "true" motivations, the terrorists were scaffolded by religious sentiments and concepts. The terrorist actions in London and Spain post-9-11 seem to be illustrations of the low-grade quasi-war that Huntington outlined in Clash of Civilizations. Whether you believe that the term "Islamism" is a term with any utility, or whether Muslims are a demographic threat to Europe, or that human rights abuses against American Muslims are a gross violation of international law, the salient fact is that the world has a Muslim problem. Muslims have a Muslim problem (see Algeria). Westerners have a Muslim problem. People confused for Muslims have a Muslim problem (Sikhs in the USA). There are other problems out there, but the "Muslim Question" is one that is I think relevant to our lives, and pretending it isn't suggests very different priorities and models of the world out there than I have. Another concept that Huntington alluded to his Clash of Civilizations was that Muslims tend to have a "U-shaped" heirarchy of loyalties, that is, a strong focus on family and tribe and the Ummah, but little affinity with particular nation-states. My posts dealing with the Salafi terror network which is the prime international locus of low-grade warfare is I think an important aspect of this, the foot soldiers have minimal attachments to any nation, whether it be a Western nation (many were born in the West or resided for long periods in the West), or any Muslim majority nation-state. Their loyalties were to their tribe, their family-by-choice that they created when they were in an "alien" culture, and a vague abstract concept of a Caliphate.

This brings me to an issue that was made famous by Huntington's book, the "Islam has Bloody Borders" observation, which many objected too. I think it is empirically warranted. But, of late I have wondered about the reason for the bloody borders. A few weeks a correspondent of Steve's noted:

Wait a minute; much of Latin America has about the same IQ as the Muslim world, and you don't see international terrorism coming from that region. Islam has bloody borders, and Latin America doesn't.

Here is a map of Huntington's civilizations:


Notice something about the borders of Islam vs. Latin America? The ratio of border to area of Islam is rather high in comparison to Latin America. The main opportunity to have "bloody borders" on the case of Latin American is actually going to be along the US-Mexican border, and I'll leave it to readers to decide whether that border has been bloody (aside from the Mexican-American War). In fact, of the large civilizations defined by Huntington, Islam seems the least compact, the most interpentrated with others. The reality is that if all Muslims were turned into Latin Americans today, I don't necessarily think that the level of intercivilization violence would be the same, I think Huntington and Steve's correspondent hold part of the truth. But though I am not a geographic determinist in the mold of Jared Diamond of H. Mackinder, I think that geographical realities determined by the historical path of the growth of Muslim civilization laterally along the 30 degree axis of latitude certainly maximizes the opportunity for conflict, and made more likely cultures which were primed toward conflict because of habits, customs and traditions formed during past wars and clashes (and importantly, we might not be able to do anything about the cultural habits accrued because of these historical-geographical conditions).

But there is another point of Huntington's which relates back to the rise of decentralized terror networks, and is in many ways an extension of what he said in Clash of Civilizations, in that Islam has no core state. A core state is a dominant state of a civilization. For Sinic civilization that is clearly China. For Hindu civilization that is clearly India. For Orthodox civilization that is clearly Russia. Western, Latin American and African civilization do not have core states of such paramount clarity, though the United States and South Africa could make claims in the West and Africa. Islam on the other hand doesn't really have a proto-core state. Indonesia is large, but a great deal of its population is heterodox and it is distal to the central of gravity of the Islamic world. Egypt is central in geography and history, but its population is not greater than other rivals, such as Turkey or Iran. Saudi Arabia is hampered by its particularist Salafi creed and pro-Western monarchy. Pakistan is South Asian. Iran is Shia. Turkey has a secularist elite. And so on. Nevertheless, though Huntington gives the nod to low-grade war as being the operant condition in the clash between the West and Islam, he does not transcend the tendency to think in terms of nation-states. That is, he does not seem to see the importance that transnational networks of passport nomads and pariahs will play, outside, above, and beyond the sponsorships they might have once received from a particular state. While Huntington still wishes to focus on the macroscale civilizational dynamic by assembling a veritable army of details that point to his thesis that civilizational affinity matters (many of them disputable, and some subsequently falsifiable over the past 8 years), he gives short-shrift to the intracivilizational conflicts which simmer and often boil over.

This is where we get back to Catlos' book. The historical background to the collapse of Muslim Spain was fundamentally about the weakness of Muslims as much as the revival of Christians. After the collapse of the Ummayad Caliphate in Al-Andalus hundreds of taifa emirates emerged. This political pluralism gave birth to an efflorescence of cultural production, but, it also endgendered relative weakness vis-a-vi the formidable marcher states of Castile, Leon and Navarre. The larger Christian polities simply began to swallow up the Muslim emirates, who were too busy jocking for power amongst themselves to see the larger scale dynamic. Once they did see the threat from the north they couldn't agree upon a common front, and instead made recourse to intervention from dynasts in North Africa, first the Almoravids, and later the Almohads. These two Berber dynasties were culturally very distinct from the Muslims of Al-Andalus, and they alienated their new tributaries as much as they fought the reconquista states. In the end, rebellions and lack of cooperation from Spanish Muslims resulted in the inability of the North African dynasties to mobilize the population and state in defense against the Christian kingdoms. Nested within the intra-Muslim squabbles, there were conflicts between various Spanish Muslim groups, from the elite blooded Arab families, to converted lineages who dated back to the Visigothic period, and to Berber stock. Within the group of Muslims of Aragon, who were all Arabic speaking and non-elite (as elites who did not convert emigrated, as I noted above), there were still divisions along the lines of class and status. The conflicts noted above were easily mirrored by the Christians. The point is within the putative signal of intercivilization conflict there is a veritable cacophany of intracivilizational conflict. The famous alliances between France and the Ottomans, or Richelieu's diplomatic bias toward the Protestant princes of Germany against his fellow Catholic Hapsburgs, simply illustrate the principle that within the noise of intracultural conflict there are many openings for making friends from afar. Catlos' work is a close examination of this phenomenon. The relatively benign attitude of northern whites toward southern blacks, and contempt for southern whites (granted, this was always exaggerated), is another illustration of the principle at work (I have read enough literature that surveys the 19th century to contend that this stereotype extends very deep into our historical past).

All of this does not mean that there aren't tensions along civilizational lines. There is a persistent signal within the noise. The key is how strong that signal is, and its strength is contingent upon multiple factors. If, for example, there was universal equality of wealth, freedom from want, and endless opportunity for individual self-realization, would that usher in a utopia of peace and providence? No, I hold that there might very well be a strengthening of the signal of discord based on values and ideology. When first order needs on the individual level are sated, I hold that other considerations, ostensibly more lofty, come into play. As I have noted multiple times, a large (disproportionate) number of the Islamic terrorists who claim to assail the West come from wealthy, healthy and intellectual backgrounds! The poor, the indigent and the illiterate often have greater concerns on their plate than a "clash of civilizations."

But as I have emphasized over and over implictly, this isn't physics. Hell, it isn't even genetics. The noise is overwhelming, even though a disproportionate number of terrorists in the Salafi network come from affluent and technical backgrounds, not all do, the North Africans tend to skew toward the lower ends of French society, perhaps even amongst the North African origin French themselves. Being illiterate and poor might prevent fundamentalism, but it would also prevent the formation of cross-cultural ties, so in the event that someone from that background rises in status, they might not bring any cosmopolitan values to the table. And yet of course we know that men like Osama bin Laden and Mohammad Atta had been around the world and seen what was to be seen. The intersection of necessary and sufficient conditions for Muslim terror have not been properly characterized. Huntington's emphasis on larger civilizational units seems to neglect the reality that intracivilizational noise and anomie are often more important to the individual than enemies afar. Catlos' work that shows the importance of cross-linking relations and the relative ineffectuality of ideology and myth in motivating and generating solidarity neglects the reality that the illustration of the importance of noise within the system presupposes that there is a signal in the first place, in other words, all things being equal, Muslims are still Muslim, and Christians are still Christian. Of course, all things are rarely equal. I have emphasized on this blog repeatedly that reality as it really is on the substantive level is often far less relevant than reality as it is perceived in the minds of individuals. After reading books and articles on marriage, and hearing from authors how Christian values as espoused in the New Testament were crucial to the "Romeo and Juliet revolution," I was amused to stumble upon an evangelical Christian Indian who was arguing that "arranged marriage is the Biblical model." 'tis the nature of the beast I suppose. In the short term whether Islam is naturally violent is irrelevant, the reality of the Salafist network must be addressed. I am not one who thinks this is an existential threat, but I do think how we respond to the threat will help determine the evolution of our culture, Western culture.

The irony about Clash of Civilizations is that conflict between civilizations is only worthy of study because Huntington passionately cares about the core values of the West, pluralism of ideas, individuality and basic human rights. His message is clearly aimed at waking up the West, and arguing that the Western Moment is over, that the dream of a Universal Civilization as depicted in Francis Fukuyama's The End of History and the Last Man has not, and will not, be validated. I think Huntington is too pessimistic. I have covered many topics in this post, so I won't elaborate why I think Westernization is a reality, but I do think that the world is being unified by a common Western matrix, though there are regional flavors and variations. But Huntington's message is that the ultimate threat comes from the lack of focus and passion that he perceives in the West, the unilateral cultural disarmament in the face of non-Western memes and the evisceration attempted from within by an assorted motley. I believe how the West responds will help determine what shape the coming Universal Civilization takes. The reality is that in the West vs. the Rest, the Rest are simply epiphenomena who will help shape the temporary dynamic. But epiphenomena can be a short term bitch.

1 - The exact details are somewhat confusing. Suffice to say that some Moriscos who were of Christian religion were also expelled, while a large number who had converted over the centuries had assimilated and were not expelled (some of the most enthusiastic boosters for expulsion from long established Morisco families who disliked being associated with crypto-Muslims), while the vast majority of those who refused to abandon Islam in secret probably left. Nevertheless, Morisco bandits are attested to as late as the 18th century in the hills above Granada.

Google news query for HapMap. Dienekes links to some of the prominent ones. HapMapistry from gnxp posts past.

I have just learned something new. Or, rather, become newly aware of the implications of some things that have been rattling around in my mind for a while. Greg Cochran linked (indirectly) to this quote:

The loci in question are so tightly linked that rare recombinants practically never arise - this explains why the different multi-locus genotypes appear, when crossed, to segregate like single locus genotypes. A set of genes so tightly linked that they behave like a single locus has been termed a supergene.

This was a eureka moment for me. I have sometimes wondered about the evolutionary implications of chromosomes. I'm sure that there's a molecular reason for them - certainly, it would be hard to imagine a diploid genetic architecture, necessary for sexual reproduction, without them! But having said that, it would seem that chromosomes only get in the way of sexual reproduction: If sexual reproduction is about facilitating genetic recombination, then more would certainly be better than less, and we know that many other species have many more than our 23 pairs: horses have 32, dogs have 49, ferns have 630! So why haven't we evolved the maximum possible number of chromosomes? It's certainly possible to have a lot more chromosomes than we have.

Clearly, it seems to me, the answer is that sexual reproduction is not always a good thing. Rescrambling our genes every generation has the effect of breaking up favorable combinations of genes, so it must be that a small number of chromosomes is an adaptive response to this. Genes on the same chromosome get rescrambled not every generation, but once out of many generations, with genes closer together getting rescrambled less often than genes farther apart. The infrequency of the rescrambling makes time for selection to weed out unfavorable linkages as they arise.

Some predictions:

1. Linkage disequilibrium is not necessarily a sign of recent positive selection - it could also be a sign of coadapted gene complexes.

2. Coadapted gene complexes that involve genes on different chromosomes would have to be much more advantageous than those involving genes on the same chromosome, in order to be maintained.

3. The advantage necessary to maintain coadapted gene complexes varies according to the physical distance on the chromosome of the genes involved. (I know it's a bit more complicated than that, but roughly.)

4. A reduction in the number of chromosomes could be adaptive if it locks-in a favorable gene complex.

5. A coadapted gene complex could also explain this, as these genes don't recombine.

6. This could be part of the answer why we have sex so often (i.e. more often than models would predict)!

PS: This is another example of the importance of tradition.

(Cross-posted at Rishon Rishon.)

The Case for Selection at CCR5-Δ32 isn't as strong as some would have you believe according to this article. They don't rebut that selection could have resulted in the spread of this allele, but they contend that a neutral hypothesis can not be rejected by the data on hand.

Related: Diffusion of HIV resistance.

Genes such as G6PD, ASPM, and hemochromatosis are known to be undergoing strong positive selection in humans. You see a high-frequency variant with next-to-no variety and lots of linkage disequilibrium.

If you had to guess, what fraction of human genes would you expect to be currently experiencing such strong positive selection?

Kate over at Outside the Beltway has a unique analysis for solving Canada's problems with handguns. She notes the futility of Prime Minister Martin asking Secretary Rice to have the Americans do something about gun smuggling. She notes that the Prime Minister's office is preparing a series of gun-control initiatives but that it is unlikely that a meeting with the Jamaican Prime Minister about restricting the supply a trigger pullers will be unveiled:

No less than 47 of the Jamaican-linked gang were arrested and more than 1,325 charges were laid.

The gang was the longtime rival of the Crips, another organized-crime street gang with Jamaican background.

So, what happens the day after the police and local politicians congratulate themselves for a successful investigation and massive raids?

Why, on Friday -- the very next day -- there were five shootings, with three of them fatal.

[ . . . ]

So, what do we do in such a discouraging situation?

Well, you just can't keep sitting back and coming up with excuses. Such as Ontario Liberal Premier Dalton McGuinty's chant about "American guns on Canadian streets," with the full backing of NDP socialist David Miller -- known to many as Mayor Useless. And there's Toronto rookie police Chief Bill Blair claiming that half the weapons used here by criminals are smuggled from the U.S.

However, on Thursday, U.S. Ambassador David Wilkins knocked those claims by noting that most of the guns coming from the U.S. are actually bought there by Canadians and smuggled back here. In other words, where are Canadian customs and other border-watching authorities?

The truth is that Canada continues to suffer from a longstanding policy of federal Liberal governments going back to 1965. That's when the Pearson-Trudeau government loosened the Immigration Act to make it much easier for previously unqualified foreigners to enter the country and stay on as new citizens. The criminal elements came right along with them. And the Liberals got most of their votes.

The Liberals also weakened the criminal justice system. They got rid of capital punishment, provided early parole, built prisons that are more like country homes and introduced a Young Offenders Act that made youth crime a sick joke.

Former Toronto police chief Julian Fantino pushed for a mandatory 10-year sentence for anyone using a gun to commit a crime. But he ended up being pushed out by Mayor Miller, who prefers the soft, social-worker approach in handling criminals.

Over on the Mises Economic Blog, Lucretius, a neurobiologist, has written a post rebutting the contention put forward by Joshua Greene and Jonathan Cohen in their paper For the law, neuroscience changes nothing and everything that:

New neuroscience will change the law, not by undermining its current assumptions, but by transforming people’s moral intuitions about free will and responsibility. This change in moral outlook will result not from the discovery of crucial new facts or clever new arguments, but from a new appreciation of old arguments, bolstered by vivid new illustrations provided by cognitive neuroscience. We foresee, and recommend, a shift away from punishment aimed at retribution in favour of a more progressive, consequentialist approach to the criminal law.

I'd encourage you to read the philosophical musings being entertained but also keep in mind the news breaking in Japan today in which Nippon Telegraph & Telephone Corp. researchers demonstrated a rudimentary ability to control volunteer subjects via remote control:

A special headset was placed on my cranium by my hosts during a recent demonstration at an NTT research center. It sent a very low voltage electric current from the back of my ears through my head — either from left to right or right to left, depending on which way the joystick on a remote-control was moved.

I found the experience unnerving and exhausting: I sought to step straight ahead but kept careening from side to side. Those alternating currents literally threw me off.

The technology is called galvanic vestibular stimulation — essentially, electricity messes with the delicate nerves inside the ear that help maintain balance.

I felt a mysterious, irresistible urge to start walking to the right whenever the researcher turned the switch to the right. I was convinced — mistakenly — that this was the only way to maintain my balance.

The phenomenon is painless but dramatic. Your feet start to move before you know it. I could even remote-control myself by taking the switch into my own hands.

There's no proven-beyond-a-doubt explanation yet as to why people start veering when electricity hits their ear. But NTT researchers say they were able to make a person walk along a route in the shape of a giant pretzel using this technique.

It's a mesmerizing sensation similar to being drunk or melting into sleep under the influence of anesthesia. But it's more definitive, as though an invisible hand were reaching inside your brain.

[ . . . ]

If you're determined to fight the suggestive orders from the electric currents by clinging to a fence or just lying on your back, you simply won't move.

But from my experience, if the currents persist, you'd probably be persuaded to follow their orders. And I didn't like that sensation. At all.

The article goes onto speculate about the commercialization of this technology, for both civilian and military markets. What struck me about this report was how the remote control device was stimulating the senses and causing the brain to induce action, but instead of free will being the agent of initiation, it was an external electrical current acting on the nerves and initiating the cascade of processes that followed.

From The Genetic Basis of Evolutionary Change:

For many years population genetics was an immensely rich and powerful theory with virtually no suitable facts on which to operate. It was like a complex and exquisite machine, designed to process a raw material that one had succeeded in mining. Occasionally some unusually clever or lucky prospecter would come upon a natural outcrop of high-grade ore, and part of the machinery would be started up to prove to its backers that it really would work. But for the most part the machine was left to the engineers, forever tinkering, forever making improvements, in anticipation of the day when it would be called upon to carry out full production....

Some have said than in the first 5 years of the allozyme assay era more data on the the genetic structure of populations was accumulated than had been in the previous 100 years of pre-molecular experiments and observations. Anyway, evolutionary genetics is still a work in progress, and I don't have much time to comment right now, but I thought I'd point you to this paper in PLOS Genetics, The Evolutionary Value of Recombination Is Constrained by Genome Modularity. Since biology is the science of exception riddled generalizations, take the paper with a grain of salt. What is applicable on the microorganismic level might not be applicable on the multicelluar scale (i.e., selfing and asexuality are long term fitness optimizing for example). Additionally, I also suggest you check out the most recent issue of issue of Journal of Evolutionary Biology, it is all about adaptive dynamics.

Related: Through the Rugged Roads of Gene Land.

Armand Leroi has a nice fluffy piece, On Human Diversity, in The Scientist. Leroi is one to keep an eye on because he is in John Brockman's stable, and his creatures tend to become public intellectuals rather quickly. One thing though, why is a developmental biologist pushing this? Neil Risch should be stepping up! But I have a sneaking suspicion that the devo will always win over evo in a war of words since the devo people can trot out 10,000 definitions to describe the progression of a zebrafish eye while the evo people can only jot down some befuddling equations. Hat tip to Jay.

Update: Go read this post from Future Pundit, Genetic Analysis Shows Signs Of Selective Pressure In Human Evolution. By the way, doesn't the researcher look like a baby? Of course, Brad DeLong looks like a baby too.

Update II: Also, check out Derb's piece in NR, The Specter of Difference.

Many are the journals that I read. Any recommendations to add to the list? A bias toward human evolution and genetics preferred. You should also check out Jason's megalist.

Over the past week I've been sampling chapters out of Mark Ridley's Oxford Reader anthology, Evolution. I can't recommend this book enough! It runs the gamut from historically oriented essays dating from the late 19th century all the way to cutting edge papers from the past 10 years. Ridley manages to balance accessibility to the general audience with rigor and relevance that would appeal to specialists. In my opinion general interest science books geared toward the lay audience are often too skewed toward biographical minutiae as opposed to the ideas which are the ends of science. Many popularizations of books on evolution don't have any basic math which succinctly generalizes and summarizes the verbal concepts being exposited.¹ By basic math, I mean some simple algebra, evolutionary biology isn't particle physics, you don't need to get into diffusion equations to model how alleles spread through a population at the most elementary and approximate level. In Evolution there is enough math to wet the appetite of those who wish to seek more technical treatments of the topics surveyed, instead of redigesting the science prior to presenting it for your consumption Ridley samples a small portion intact. I'm definitely going to check out the other Oxford Reader's books out there in the hopes that the quality wasn't just due to Ridley (I'll start with the Classical Philosophy anthology since I know a bit about the topic and so can judge whether there is a quality drop off).

1 - Of course general audience books on "evolution" almost always skew toward macroevolution because it is a topic with more charisma than microevolutionary dynamics, which, being derived from population genetics means some math is a must for genuine internalization of the concepts. But even in macroevolution there are now mathematical models cropping up, see Evolutionary Dynamics.

Dr. Manuel Casanova has done some interesting research on neuronal minicolumns and autism. From the summary of Abnormalities of Brain Circuitry (Minicolumns) in Autism:

[The] neocortex is formed early on during gestation by the supernumerary aggregation of modules. The smallest module capable of processing information is called minicolumns. These modules or minicolumns are composed of both cells (neurons) and their projections which together form standardized circuits. Recent studies suggest that minicolumns may be abnormal in autism. More specifically, the brains of autistic patients have minicolumns that are smaller and more numerous than normal. Furthermore, the cells (neurons) within each minicolumn are reduced in size.

Since the metabolic efficiency of neuronal connectivity is a function of cell size, the presence of smaller neurons in the brains of autistic patients has a dramatic effect on the way that different parts of the brain interact with each other. Functions that require longer projections (e.g., language) may be impaired while shorter ones (e.g., mathematical manipulations) may be preserved or reinforced.

Furthermore,

In autism, smaller minicolumns in brains that are, on average, larger than normal suggests their total increase in numbers....

What is the meaning of smaller minicolumns? First, this question has been approached from the standpoint of computer modeling by a group in Switzerland (Dr. Gustafson’s). Results suggest that smaller minicolumns tweak information processing in favor of the signal. By comparison other conditions characterized by larger minicolumns (e.g., dyslexia) tweak information processing in favor of noise. This means that autistic individuals usually do well in processing stimuli that requires discrimination while dyslexics are better at generalizing the salience of a particular stimulus.

Second, minicolumns are compartmentalized. Information is transmitted through the core of the minicolumn and is prevented from suffusing into neighboring units by surrounding inhibitory fibers. The inhibitory fibers act in analogous fashion to a shower curtain. When working properly and fully draping the bathtub the shower curtain prevents water from spilling to the floor. In autism minicolumnar size reduction involves primarily the peripheral compartment that provides the inhibitory surround.

This means that stimuli are no longer contained within specific minicolumns. Stimuli overflow to adjacent minicolumns thus providing an amplifier effect. This may explain the hypersensitivity of some autistic patients as well as their seizures....

Minicolumnar size is not the only abnormality observed in the neocortex of autistic patients. It appears that cells (neurons) within individual minicolumns are also reduced in size. This has important consequences in terms of connectivity. Long connections require the metabolic sustenance of large cell bodies. A neuron in the brain that connects all the way to the lower spinal chord requires a fairly large cell body. By way of contrast, a neuron whose projection remains within the cortex, contacting a closely adjacent cell, can manage its metabolic demands with a small cell body.

The small cell bodies in the brains of autistic patients favor information processing through short intra regional pathways, e.g., mathematical calculations, visual processing. Similarly, cognitive functions that require long inter regional connections would prove metabolically inefficient, e.g., language, face recognition, joint attention.

More on autistic brains: The essential difference and Male brain ~ more sons vs. female brain ~ more daughters?

More on minicolumns: The minicolumn hypothesis in neuroscience

I often get asked about questions regarding the size and development of the human brain in the evolutionary context, and I have a hard time remembering the material on allometry and what not that I've read here and there.¹ But The Journal of Human Evolution has a nice paper up, Human encephalization and developmental timing, which I've put up as a PDF in the GNXP forum files as "encephalization."

1 - My primary source in The Symbolic Species, though I've read other stuff in the literature....

Sometimes readers ask about massive chromosomal reorganizations and what not. I don't know enough that I feel comfortable commenting, but I noticed this review, Chromosome evolution in eukaryotes: a multi-kingdom perspective, and have placed it in the gnxp forum files as "chromosomeevolution."

Over a week ago I alluded to the mid-20th century debate between the Classical and Balance Schools of evolutionary genetics. I used this example specifically because I suspect many readers have an interest in evolutionary genetics and so would find the example extremely illustrative of my general point. But, in hindsight it was perhaps a somewhat obscure reference, and I will first clear any remaining obscurity, and then indicate more explicitly why I focused on this "controversy" in relation to my belief in science in general.

If the Classical vs. Balance School debate is old hat for you, skip ahead. If not, here is the sketch:

• The Classical School envisages that in a given population the vast majority of loci are fixed. That is, greater than 99% of alleles on a locus in a population are identical.¹ Polymorphism, where more than 1% of alleles are non-modal, is an epiphenomenon which is observed because transitions between two alternative alleles where one is being driven to fixation by directional selection take a number of generations (dependent on strength of selection). The vast majority of mutations in this school of thought are purified via negative selection, functionally constraining loci toward a monomorphic condition. Additionally, a few mutations are selectively advantageous and steadily driven to fixation. One could imagine that over evolutionary time a locus would generally be monomorphic, but periodically when a new mutation that was advantageous arose it would result in a transitory circumstance of polymorphism as the locus shifted from fixation on the "ancestral" allele toward fixation on the "derived" (mutant) allele. In the Classical School roughly 1% of loci might be polymoprhic, which in reality would simply be a "snapshot" taken during one generation (so in the future a different 1% would be polymorphic as different mutations would be in the process of being driven to fixation).²
  
• Roughly speaking the Balance School assumed that the rate of polymorphism in the population would be higher than in the Classical School, for example, 10% of loci might be polymorphic. The central reason offered was hybrid vigor or overdominance/heterozygote advantage. In this situation obviously polymorphism would have to be maintained in a population if heterozygotes were more fit than homozygotes since the fixation of any allele would expunge heterozygosity from a population. If homozygous individuals were of equal fitness and heterozygotes were more fit than homozygotes, then the frequencies of two alterative alleles, p or q, would have to be 50% to maximize the number of heterozygous individuals (p² + 2pq + q² in Hardy-Weinberg Equilibrium). There are other ways that diversity could be maintained, for example, frequency dependent selection where fitness is inversely proportional to frequency. Additionally, population substructure, migration and variation in fitness contingent upon local ecological conditions could all combine to maintain polymorphism.
  

The short of it is that both schools were very wrong. In 1966 a famous paper by Lewontin and Hubby³ showed via molecular methods that levels of allozyme polymorphism were far higher than predicted by either school of evolutionary genetics. Enter the Neutral School.

• The Neutral Theory basically contends that the rate of molecular evolution is dependent upon the rate of mutation.⁴ Roughly speaking it agrees with the Classical and Balance school that the many mutations are purified from the genome (proportion depends on the amount of "junk" in an organism's DNA, nonsynonomous mutations would be purified obviously), but, it suggests that the vast majority of substitutions on a locus of one allele for another are driven by neutral random walk genetic drift rather than positive directional selection or balancing selection. As in the Classical School polymorphism assayed via molecular markers is epiphenomenon, in reality you have a situation where a given locus that is polymorphic is transitioning between allele A and allele B, you simply happen to be sampling between these two alternative fixed states (obviously random genetic drift would not result in fixation at the same pace as directional selection, so a far higher proportion of loci would be in the "transient" polymorphic state). This sort of random walk process is ubiquitous throughout the genome and many molecular geneticists would contend that to the first approximation Neutral Theory holds as the best predictive model for the dynamics of evolution on the genomic scale. Neutral Theory has become the ideal null hypothesis against with selectionist models are tested.
  

Frankly, both the history and the science of this "debate" fascinate me, but I will exercise self-restraint and spare you further details. While Kimura was the doyen of Neutral Theory, one could consider Sewall Wright the central figure in the Balance School and R.A. Fisher the primary thinker who anchored the Classical School. Wright and Fisher were brilliant men, they seeded many of the theories from which the Modern Synthesis of Neo-Darwinism took sustenance. Theodosius Dobzhansky and Ernst Mayer relied upon Sewall Wright's mathematical models to frame their experimental and observational data in generating their evolutionary genetic world views (and these two were in many ways gatekeepers for the American public to the halls of evolutionary biology, just as Julian Huxely was in Britain). Fisher's ideas served as the foundation for the Oxford tradition of ecology and genetics, furthered by E.B. White in ecology and W.D. Hamilton in social evolution and genetics and popularized in a broad sense by Richard Dawkins.⁵ Nevertheless both traditions were thoroughly blind-sided by Lewontin and Hubby's initial results from the allozyme assays.

In a sense I think though their mistakes were different in character. The Neutral Theory in many ways undercuts the theoretical basis for the contention that heterozygote advantage of some sort is the primary means for the maintainance polymorphic diversity, an idea that is central to the basic thrust of the Balance School. If you assume the Balance School's thesis as to the fitness advantage of heterozygosity and then plug in the number of segregating polymorphic loci that have been empirically verified (or even assume a conservative number extrapolated from the data), then you quickly get some ludicrous differentials (dozens of orders of magnitude) between super-heterozygous individuals and the population mean fitness (that is, heterozygous and homozygous across many loci).⁶ Heterozygote advantage is an omnipresent idea in evolutionary biology, but many scholars have a hard time finding many indisputable empirical cases (Sickle-cell anemia and MHC are the primary ones).

In contrast the misconception of the Classical School was founded on simple ignorance as to the true empirical realities of genomic architecture in the pre-DNA age. Remember, these ideas and distinctions were hashed out between Fisher, Wright and their respective acolytes in the 1930s, well before Watson and Crick had presented their theory regarding the structure and function of DNA. Richard Dawkins has offered in his many popularizations that the Classical School addresses a different subject than the concerns of Neutral Theory. The focus of selectionist theorists in the tradition of Fisher has always been on the genetic architecture of loci which are functionally relevant. In other words, genes which influence phenotype and fitness. The fact that most of the genome of most organisms seems non-functional in the Central Dogma fashion is irrelevant to selectionists, molecular evolutionary dynamics is simply outside the purview of scholars in the Classical School.⁷ Both Fisher and Hamilton witnessed the rise of molecular biology (especially Hamilton), but did not believe that it was particularly relevant to their concerns (see R.A. Fisher: Life of a Scientist and Narrow Roads of Gene Land: Volume I). Their basic model did not entail moving much beyond the fusion of Mendelian and the biometrical quantitative genetics which Fisher triggered with his 1918 paper, The Correlation between Relatives on the Supposition of Mendelian Inheritance.⁸ As detailed in The Darwin Wars selectionists tend to use words like "gene" in a very specific and precise fashion, and much of the discourse between those who come out of the Oxford School and others influenced by Neutral Theory is a debate around semantics and ownership of a particular word (a word that has magical properties when it comes to public recognition). Dawkins and the selectionists tend to acknowledge this implicitly, though to my eye he has an annoying tendency to pretend as if somehow selectionists won the debate when it was more like a disagreemant due to the fact that the two camps spoke in sharply different dialects. The public simply tends to get confused and can't be expected to follow along very easily (there are some like Stephen Jay Gould who did plainly disagree with Dawkins, but unlike real neutralists Gould was a verbalist and not a modeller, so confusion and miscommunication were the order of the day, not an unfortunate byproduct of the process).

The overall point is that evolutionary biology is still around, and evolutionary genetics is a vibrant field, even though the giants of the discipline were ignorant as far as the details of how the genome of most complex organisms actually worked. This ignorance led to the Classical School's surprise as to the modal non-selectionist implication of any given segment of an organism's genome. The fact that synonomous point mutations result in the same amino acid was not something that R.A. Fisher, or Sewall Wright, would have been able to anticipate since the basic atom of genetics, DNA, wasn't part of their knowledge base. Even conceding neutrality, Tomoko Ohta's Nearly Neutral Theory shows how deleterious alleles might often be fixed in populations, in contravention of both the Classical and Balance School's (and of course, classical Neutral Theory) faith in the power of purifying selection. Understanding the genome at its most basic base pair level opens up a whole new field of implications and theoretical possibilities that were closed off to the traditional pre-DNA population geneticists.


This survey shows that science does not always work via the selection of competing hypotheses, rather, sometimes the data compels the emergence of new theoretical models and renders the old paradigms obsolete on a fundamental level. Molecular evolution is more fundamental than the phenotypic evolution that selectionists focus on, because evolution of the functional genome is a subset of evolution on the genome as a whole. Nevertheless, the pushing aside of older models as fundamental units of understanding does not mean that they are no longer useful. Both Sewall Wright and R.A. Fisher spent the 1920s outside of academia and were focused on applied quantitative genetics. Agricultural genetics is surely benefiting from modern genomics, but that does not mean that older methods of breeding premised on quantitative genetics which goes little beyond the biometrical thesis of the early 20th century are unnecessary or unprofitable. A better example is Newtonian Mechanics. As a theory of gravitation General Relativity has superseded it, but in the vast majority of situations Newtonian Mechanics is an exemplary approximation to reality. It is a banal observation that natural science is the progress of sequentially more precise, accurate and abstractionally deeper theories about the world around us. R.A. Fisher's ideas about the fundamental nature of additive enetic variance as being the parameter that undergirds evolution might be an idea that is past its best days on a fundamental level, but the model still has great utility, explanatory power and it is an accurate fit on an important subset of evolutionary phenomena. Similarly, Sewall Wright's ideas regarding the ubiquity of balancing selection via overdominance might be empirically falsified, but his other ideas coupled with this thesis as regards a rugged and irregular adaptive landscape are only now being pushed beyond verbal metaphors via more advanced analytic, and importantly, computational techniques. There may come a day when Neutral Theory and its molecular evolutionary spawn may seem less fundamental, and we might be able to establish more order and precision in our understanding of the variables that drive the rate of mutation.

But a major problem that always crops up is when there is a transition between the scientific discourse and the popular discourse. There are multiple interactions at play here. First, between scientists, second, between scientists and the public, and third, between individuals in the general public. Consider the debate around "gradualism." Stephen Jay Gould and Richard Dawkins spent much of the 1980s duking it around this particular topic. Its importance as an organizing principle in terms of paradigm affiliation can be seen in PZ Myers' comment about evo-devo guru Sean Carroll's book Endless Forms Most Beautiful, as he says, "It also takes a very conservative view of evolutionary theory." What exactly could Myers be talking about? If you read Carroll's book I think it is clear that he doesn't want to be interpreted as offering an opening to macromutationist thinking, the type that crops up in the works of the late Stephen Jay Gould, a personal hero to PZ Myers. Though I lean in Carroll's direction as to the merits of the case, even I thought he was being a bit monomaniacal on this issue, but the key is that Carroll was addressing a lay readership and he had clearly had bad experiences with his research being distorted when transmuted for public consumption. Words have different meanings in different contexts. What exactly does "gradual" mean? In The Blind Watchmaker Richard Dawkins dismisses puncuated equilibria as simply a subset of the standard model proposed by evolutionary traditionalists. I think in many ways Dawkins is correct, but a deeper problem is the use of terms like "gradual" across the chasm of opinion. What exactly is non-gradual on evolutionary timescales? To be precise, if you took a quantitative character (i.e., height) and plotted it against number of generations since time t, what distinguishes gradual change vs. non-gradual? Is there a particular first derivative that needs to be detected at some point in the function to cross the threshold of gradualism? Has anyone agreed on the exact measure? Taken outside of a scientific context one can imagine how ludicrous and incomphensible this sort of discussion can get. Since one can't expect the public to know calculus I think the easiest thing would be to publish gradualist vs. non-gradualist books with a large number of figures which plot trait vs. generations. I think scientifically the debate comes close to being worthless, but certainly controversy sells a lot of books, and scientists are humans with egos and bills to pay.

Sometimes the confusion isn't even a structural bias in the way verbal transmission occurs, rather, it is a conscious attempt at obfuscation. For example, David Berlinski recently attempted to imply that Motoo Kimura's Neutral Theory casts doubt on the power of selection in driving evolutionary change. Berlinski claims to have worked in molecular biology laboratories when he was at Princeton (Ph.D., mathematics), so I can't believe he thinks that Kimura's ideas about neutral molecular evolution deny macroevolution. Creationists (or Design advocates, whatever they are called now) attempt to make a distinction between microevolution and macroevolution whenever it suits their case (i.e., "that's not evolution, that's microevolution! I don't deny microevolution."), but in this case they gloss over distinctions within the genome which would make more intelligible neutrality in the context of these two processes because it serves their case of "debunking" Darwin. Similarly, though a whole cottage industry has arisen that destroys the "Nature vs. Nurture" dichotomy, those who "lean toward Nurture" (a common assertion across the political spectrum) never fail to construct the strawman to tear it down. In part it is politics as it makes the rhetoric more devastating, but I suspect in part it is a property of how the human mind works, as it needs to think in terms of types instead of expectations, variances and deviations.

This finally gets me back to the ideas that I expressed in The True Believer revisited.... and I am a believer. Science is a special enterprise in terms of its character and the yield of its ideas in material terms. But, it is still a human enterprise, and conventional cognitive, social and cultural biases are still at play. If you compare scientific culture, unified by journals, conferences and common rites of passage, to the culture of a particular religion, you seem similarities. Unfortunately, specific religions are transient, and always shifting in character. So if you take analogy far enough scientific culture itself is going to be subject to historical forces contingent upon the human condition. Intersect this with the empirical reality that genuine scientific culture, unlike religious culture in general, is not a human universal, and an exceedingly rare event in the history of the human race, then you have grounds to worry...if you value science. Though few people (i.e., less than 10% of the population) value science for the sake of science, most people appreciate its importance in scaffolding the consumer society with gadgets, goodies and tools which allow us to sate our acquisitive passions and buffer us from the vicissitudes of nature. Stipulating the utility of science, I was expressing a world view where I thought that one should acknowledge that scientists are humans and so find ways to augment scientific culture's functional robusticity in the midst of non-scientific culture.

Which takes me to religious analogies and organizations. I am generally skeptical of functional explanations in anthropology, which assume that groups have their own higher order properties which allow them to survive no matter the details of human traits. Nevertheless, the Roman Catholic Church and the world Jewry have survived as distinctive entities for the past 2,000 years.⁹ My thought was simply, first, "What lessons can we learn?" "We" meaning those of us who privilege knowledge acquisition and preservation higher up in our priorities than is modal for humans. What emotional and psychological tendencies can we mimic to make our human natures a boon for our culture rather than an obstacle toward its full realization? How can we maintain a sense of elan? Self-worth? How do we encourage "conversions," and discourage defection? My questions are all predicated on the thesis that science is a cultural enterprise. It is an enterprise with a particular fruitful system, which scientists themselves are aware of. Recently I read a paper on gene duplication and its evolutionary relevance which explicitly used Popperian terminology in laying out the framework for falsification of their hypothesis. But clearly there was science before Popper! Ironically, my impression is that in philosophy of science strict Popperism is a minority position, with the ascendence of thinkers like Imre Lakatos, Paul Feyerabend and Thomas Kuhn. I suspect that the typical working scientist will only have heard of Kuhn of the three listed. I have pointed to the research of Daniel Kahneman and Amos Tversky because they have found that scientists are guilty of the same logical and statistical fallacies as everyone else (and of course, it shocks you that medical doctors can't grasp the implications of Bayesian probabilities, no?). Scientists are almost always smart when it comes to the g factor, but, often that just means that they do stupid things really fast and express stupid opinions in a less transparently facile fashion (this generalization applies to the high g in general). What saves scientists is that sophistry is not the summum bonum of their enterprise, and the objects of their study are amenable to spare and prickly techniques which generate a far stronger than normal signal to the noise of human bias and confusion. The objects of scientific study, the natural world and its manifest phenomena, are the saving graces, the guardian angels, of the humans who espouse science as their vocation and passion.

These objects and phenomena which are the ultimate ends of scientific exploration are not a fixed constellation, and our understanding of them at the deepest level is almost never intuitive. We are like catfish at pond's bottom, gleaning the light on occassion when the murk clears and we are not busy rooting away in the mud, searching for tasty rotting things. This is one crucial way where the ends of science are radically different than, to continue the analogy, the Catholic Church or the Jewish people. The latter cultures exalt a transcendent mystery which triggers and coopts cognitive modules which are embedded in the unconscious fast & hard regions of our brain. I have repeated multiple times Scott Atran's report in his book In Gods We Trust that to a great extent religious beliefs are immune to conventional falsification via logical argumentation or data which contradicts the validity of central axioms. From a cognitive perspective I believe Intelligent Design always operates from the high ground and is flanked by deep dark forests that resist the assaults of axe and fire. Only through persistent verbal suasion at the mildest and elitist brow-beating at its extreme can scientists win the argument against religious truth claims (and most often, to "win" means that religion simply changes its tune and claims victory, and everyone politely ignores this). Philosopher Daniel Dennett has been saying that Darwinism is the "universal acid" that will eat away at all ideas, including religious ones. For a variety of reasons I disagree with Dennett, but a primary one is that we already have a better candidate for a "universal acid," and that is the capitalist system. Unlike science, capitalism engages our first order wants and appetites, it sates deep seated cognitive biases, and easily generates new ones. Science might be the hot girl who is going to make you wait 10 years for action, but capitalism is the decent looking chick who is open to being done front door and back after 10 minutes of chit-chat. How can you compete with that? Some of us are romantics and prefer a courtship with a beautiful girl who produces civilization to the short term "rational" play of slam-bam-thank-you-mam with a mid-range hottie, but this is not the modal response. Let me grant that my previous sentences were drenched in norms. So be it, I have higher order values, sue me. To parphase Hume, science is, and ought only to be the slave of the passions.

We are all sinners before an angry God when it comes to choosing between knowledge and epicurean desserts. And yet religion has, with mixed success, attempted to restrain our appetites in the service of a "higher good" for thousands of years. Why reinvent the wheel? Now, it is true that the ends of science are peculiar, but in some ways the analogy can be mapped with surprising fidelity. Consider the adherence to patently "false" beliefs that I described from religions.¹⁰ I plainly state that the vast majority of scientific hypotheses, and likely a good majority of scientific theories in currency as plausible, are inaccurate or imprecise in their modeling of the world around us. But what exactly do I mean? Do I have access to God's Book, where all the equations that model the world around us reside? I certainly don't, I assume that operationally the world has order and pattern, and scientific induction justifies induction. I assume that the progressive refinement of theories, and elevation of orders of abstraction, will continue, and yield up fruitful models of the universe around us, and likely also result in applications which can serve our more conventional passions. I plainly state that Fisher and Wright were wrong. I plainly state that Lord Kelvin was a genius who was wrong. I plainly state that Isaac Newton was mental and the scientist of his millennium. And yet I still believe, because what alternative is there in a demon-haunted world? The Church may be a whore, but what other hope for salvation is there in this world? Let us reform within the Church I say, and not shatter its fundamental unity and utility. Science is a mismash of contradictory, false, imprecise and incomplete theories, but the process continues, we aim to overcome our sin and attain a state of grace through the Church (read: culture). Let me state that I am the Hugh Hewitt of science on a fundamental level, it's gotten us pretty far, trust it. While Hewitt marshals trust in the service of a political party, I wish to marshal trust and any other cognitive bias and social system at our disposal in the service of a process and culture which serves as a necessary precondition for the modern human lifestyle.

A few days ago Michael noted that I am in "In so many ways a hard-headed skeptic." I think the above makes one cautious about that sort of appellation directed at me. In fact, to descend into the semantical mud I would contend that this weblog is a record of my opposition to unadulterated skepticism, the Post Modernist heresy, the Pyrrhonian Skepticism of our time. There are certainly questions about which I am rather skeptical. The term "skeptic" is often applied to unbelievers in the God-hypothesis because we are dissenters from the human consensus in regards to a question that the majority regards with ontological significance. But in many ways I am an anti-skeptic, I am deeply sympathetic to positivist projects in many realms. My interest in history is only minimally humanistic in its motivations, rather, I wish to understand how things were, and how they might be. I believe that at some point in the future when our AI gods descend from heaven that social science might actually justify the term science in substance as well as style. A rejection of skepticism is, ironically enough, not even contradictory with a position of atheism. George H. Smith in Atheism: the Case Against God makes a persistent argument that rationality must be God's judge and jury, not skepticism, which opens the door for theism and transcendent mystery. Writing in the 1970s Smith had not seen the wave of Post Modernist skepticism sweeping through the intellectual commanding heights outside of the sciences, but he was oddly prescient on the terminus of the skeptic's path, for some Christians rejoice in the post-rationalist world. And yet too much rationality can be a bad thing, Smith is a case in point as he was once an Objectivist, a movement whose faith in rationality became a faith in a rational faith and a cult of personality ("check your premises, except the Objectivist ones"). Lord Kelvin's case against an ancient age for the earth was eminently rational according to the physics of his day. The dissents from geologists and biologists meant nothing to a priest of the Queen of Sciences. One can find innumerable instances of rational hubris in science. And dare I say it, too much empiricism can also be a bad thing! In Geography of Thought Richard Nisbett makes the case that excessive adherence to common sense and pragmatic empiricism ultimately hampered Chinese exploration of the absurdities of the scientific world. Does "common sense" suggest to us that the earth is a sphere and that it revolves around the sun? The reality is that even scientists can balk at the absurdities of science, Einstein's rejection of Quantum Mechanics is a prominent case.

So shall we leave it to the savants who can balance the scales of skepticism, rationalism and empiricism? No! No man knows enough to be able to comprehend the universe. Empirically the feelings of transcendence and mystery that confront us when we gaze upon the blue-black night are justified. The system of science, the culture of science, is the only method we have to truly extract reproducible and verifiable signal out of that cosmic noise.

And I suppose that's it. I'll leave with an old Unitarian saying, "the question is the answer," and it is there I stand.

Addendum: I want to make a few things explicit, as I feel that I wasn't as clear as I should have been in the original text. In regards to the Balance School, I contend that the explanation for genetic variation implied by the model put forward by these theorists is incorrect, that is, the vast majority of variation within the genome is not due to balancing selection (overdominance, frequency dependent selection, multiniche polymorphism, oscillating environmental selection pressures, etc.). But, that does not mean that I reject that balancing selection factors are at work within populations, or that they are not important. I have read recent literature which suggests that lack of heterozygosity (i.e., inbreeding) can predict local population extinctions for many organisms. The levels of polymorphism found on the MHC loci is a very important fact which I don't discount. It is likely maintained by some sort of balancing selection, whether it be straightforward heterozygote advantage or long term frequency dependent selection (as W.D. Hamilton seemed to be proposing). What I am implying is that first, the genetic variation within a population is generally modeled best by a neutral framework. A balancing selection angle is a further refinement, but it is not the primary causative factor of the variation. Second, as I note above, the simple mathematical extrapolations of even trivial levels of fitness advantage to heterozygotes across a large number of loci imply unrealistic fitness differentials, ergo, heterozygosity is probably a boon in a very limited number of cases (MHC for example).

A second point I want to flesh out is my exposition of the prediction of the Neutral Theory that most substitutions on a locus will be due to random genetic drift. I said substitutions very specifically because the neutralists do not necessarily hold that mutations are in the generality neutral, rather, they tend to agree with the Classical School that purifying selection purges the genome. Rather, they hold that of those mutations which do get fixed the vast majority are neutral. In contrast the Classical School tended to assume that mutations which get fixed would be subject to positive selection. The neutralists do not reject that this occurs, they simply contend that of the fixation events positive selection is responsible for a only minority. Since the time to fixation of new mutants predicted by random genetic drift is usually far longer than when fixation is driven by selection, Neutral Theory naturally predicts that there will be far greater genomic variation as the transititions between monomorphic states within the population at a locus will last far longer. Finally, one last thing I have to add on to this is that many organisms have a great deal of "junk DNA," introns, pseudogenes and the like. So in this case, even most mutations might be neutral in regards to fitness since noncoding sequences do not have a clear functional implication. Anyway, I think that's about it....

1 - I follow the stricter convention for the frequency of a fixed locus in part to illustrate with more starkness the contrast between the two schools. Many would say that a 95% frequency of one allele would be sufficient for the locus to be declared monomorphic.

2 - Again, I give the 1%-of-loci-polymorphic quantity to illustrate the difference between the two schools, this controversy played itself out in the pre-DNA age, so it was more theoretical than empirical.

3 - Am I the only one to wonder what happened to JL Hubby? I see no publications after 1975.

4 - Large populations have many more background mutations, but the chance of fixation of any of these via random genetic drift is rather low. In small populations the number of mutations is very low, but the chance of fixation via random genetic drift is very high. The probability of fixation of a new mutant is defined as 1/2N, where N is the populuation size. If the mutation rate is μ, the number of new mutations per generation in a population is 2Nμ. Since 1/2N * 2Nμ = μ, the rate of new mutations being fixed is μ.

5 - J.M. Smith was also influenced by Fisher through his mentor J.B.S. Haldane, who shared many of Fisher's theoretical biases and defended their tradition in population genetics against Ernst Mayer's derision toward "Bean Bag Genetics."

6 - Please see Richard Lewontin's Genetic Basis of Evolutionary Change for a the mathematical exposition on why ubiquitous genomic overdominance seems to lead to absurd implications in regards to mean population fitness vs. the most perfect of heterozygotes.

7 - In the interests of brevity I will dodge the details in terms of whether non-coding sequences of various sequences are as neutral as they are assumed to be.

8 - With the advances in molecular marker technology I think that Fisher and the younger Hamilton's conceptions do not hold today, even though molecular biology is not the usual ends of many evolutionary biologists who dwell in the realm of quantitative and theoretical genetics, it is a crucial part of their exploratory toolkit. Even if you are breeding mice and doing pedigree analysis you'll probably employ a fair number of molecular methods.

9 - I do not think that Judaism before the time of Jesus really resembles "Judaism" as wel understand it, that is, the rabbinical tradition which crystallized in the borderlands of Rome and Persia, and was the normative Judaism between 500 and 1800.

10 - If you want to know, the experiment was simple, Christian believers were surveyed as to their axioms. They were then given some forged documents from the "Dead Sea Scrolls" whose veracity the researchers vouched for. The documents contain evidence that the core truth claims of these Christians were highly unlikely, and almost certainly distortions of the "truth." After this the respondents were asked if they believed in the veracity and accuracy of the documents, and many responded yes. But, these same individuals insisted that their axioms still held, and, averred that their faith was not stronger. The key point is that the contradictions were naked before them, but they refused to acknowledge it. The implication is that religious propositions are cognitively insulated from standard means of disconfirmation. One could posit that the results were in part due to the inability to reason logically because of low intelligence, but if this is modal in the population, same difference.

This Slate piece by David Plotz was pretty enjoyable in my opinion. Plotz highlights possible reasons why South Korea seems to be punching above its weight class in terms of human bioscience. He points to three primary factors:

1. Lack of moral debate in regards to the ethics of the enterprise
2. Brute force work hours
3. A top-down command scientific culture which keeps a focused eye on a specific goal
   

Plotz notes that 1/4 to 1/3 South Koreans are Christian, and yet there is no strong moral opposition to human bioresearch. This highlights the difficulties in inferring values and actions based on putative belief axioms when an individual is taken out of their social context. In other words, in my experience Korean American Christians are generally pro-life Republicans, and yet the powerful evangelical Christian community in the homeland does not seem particularly focused on bioethical issues. But is that surprising? My exploration of the abortion debate, cursory as it has been, suggests that there was a significant latency in the involvement of evangelical Protestant Christians in the pro-life movement after Roe vs. Wade. In Catholicism and Freedom historian John McGreevy points out that on the religious front only the Roman Catholic Church was moving aggressively toward pro-life activism in the first years after Roe vs. Wade, it just wasn't that salient to evangelicals. In fact, an article in 1968 was published in Christianity Today, the "house" magazine of American evangelicalism, that was mildly favorable toward expanding "reproductive rights" (this was the era when the governor of California, one Ronald Reagan, was signing legislation liberalizing abortion laws on the state level). Interestingly, Plotz does not point out that the past two presidents of South Korea have been Roman Catholic. But never fear, in South Korea Christians, and in particular Roman Catholics, are in general more liberal than the median individual in the populace, even the 1/2 of the society which is not religious.

As far as work ethic goes I think Plotz has a point about the importance of raw hours in regards to research in the life sciences. But it seems to me that there are many American scientists who put in 7 day-12 hour work weeks. I am not totally convinced that the difference in work ethic can explain the relative prominence of South Koreans, especially since Americans on average put in more hours and are more productive in their labor than workers in most industrialized nations (including South Korea).

Finally, the difference in scientific culture is I think a mixed-bag. From my readings in scientific ethnography what Asian laboratories gain in focus and direction in their top-down culture and deference to superiors, they tend to lose in innovative exploration of the full space of hypothetical possibilities. Funding for cloning research is a viable option today because a few Western scientists continued to push forward in this field even when it wasn't sexy or fashionable. If you recall, back when Ian Wilmut was on the front page of every newspaper in the world it was reported that his brand of animal science wasn't popular and was seen by many as a relict of pre-molecular days. Many were skeptical that the sort of cloning he managed was even feasible (the brute force replications necessary for his positive result certainly required a "leap of faith"). If the United Kingdom had a "science czar" who had wide-ranging powers in shifting funding I strongly suspect that all the monies that went to Wilmut would have been diverted to "real" biology, that is, the molecular level work which has been the driver for a multitude of new fields within the past generation.

So overall, it's a great thing that Asian nations are pushing forward applied research. But I still think that in the near future the cutting edge of paradigm shifting innovation is going to be found in the West, where, not surprisingly, many maverick scientists of Asian origin are now based. Remember, the great theoretical population geneticist Motoo Kimura was inspired to go into the field by an American scientist, Sewall Wright (see Kimura's chapter in Evolution).

De novo discovery of a tissue-specific gene regulatory module in a chordate. You can read the full paper (you should read the full paper).

Based on Body Size, Bacteria and Elephants Have Similar Metabolism, Ecologists FindUCR-led research team shows that organisms use their biochemical characteristics to overcome limitations arising from their body size

“The researchers’ analysis also shows that the rate of energy consumption per unit body mass declines with growing body size in groups of evolutionarily close organisms, such as mammals. For example, one gram of an elephant’s body uses up 25 times less energy than does one gram of a shrew’s body, accounting for why shrews have to eat more often than elephants. On the other hand, a bacterium, which is not closely related to an elephant in an evolutionary sense, consumes approximately the same energy per unit body mass as the elephant.�

This interests me because it is an attempt to discover meta-knowledge that applies to a much larger set of detailed knowledge in specific domains. I believe such re-organization of information is necessary if there is to be any hope for a human to comprehend even a small fraction of the world’s knowledge. The world has so many stories that a person can only learn a few of the most powerful.Clearly such meta-knowledge has limits. That paragraph could be re-stated to say a shrew burns 25 times as much energy as a bacterium. So the meta-knowledge both captures important information and misses important information.

I wanted to post a rejoinder to the avian flu discussion below. My response is to point out that pandemic flu need not kill very many people to have an enormous impact on our lives.

A Canadian investment firm issued a report on avian flu recently. They argue that the indirect (economic) effects of a pandemic will be devastating over and above any loss of life. Their strongest evidence comes from an analysis of the economic impact of SARS on affected countries. The world-wide death toll from SARS was small (~775 people), but its impact on GDP growth was substantial.

The Bank of Canada estimates that the most severe economic impact was in the second quarter when GDP growth fell from 3% in Q1/03 to -1.2% in Q2/03. Its estimate is that SARS cut second quarter GDP by 0.6 percentage points (Chart 1). Moderate as this estimate sounds, the effect in Toronto was significantly more dramatic, as Toronto represents about 15-–20% of overall Canadian economic activity.

Fear of infection alone will be sufficient to cause economic stagnation, and this is something to be worried about.

Update: Ronald Bailey - Bird Flu: Threat or Menace?

The Geographic Spread of the CCR5 Δ32 HIV-Resistance Allele. A picture is worth a lot of words, so....


Note the appeal to the "wave of advance" model of R.A. Fisher, you've seen it before in reference to the possibility of advantageous alleles spreading throughout populations via selection without concomitant wholesale demographic dislocations and migrations. The authors of the above article, which is freely available to all via PLOS, suggest that one possible reason that the Δ32 mutation isn't more common is that selection hasn't had enough time to operate. For comparison, consider lactose tolerance, though in Eurasia the allele that confers the ability to adults to easily digest milk products as adults probably has its origins in Northern Europe, in places like Northern India the phenotype has reached ~70% levels of prevalence. Contrary to some Aryan fantasists this does not imply that an ancient influx of Swedes transformed the South Asian demographic landscape, rather, selection knows a good thing.

Labels: disease

For a long time now I have been meaning to post my thoughts on what I see as overhyping the avian flu situation. Luckily, a reader of Instapundit beat me to it and summed up nicely a lot of my thoughts.

As a medical researcher, I want to make a gentle but sincere plea to the blogosphere to calm down this flu hysteria just a bit. The main way that flu kills is by predisposing its victims to "superinfection" by bacterial illnesses - in 1918, we had no antibiotics for these superimposed infections, but now we have plenty. Such superinfections, and the transmittal of flu itself, were aided tremendously by the crowded conditions and poor sanitation of the early 20th century - these are currently vastly improved as well. Flu hits the elderly the hardest, but the "elderly" today are healthier, stronger, and better nourished than ever before. Our medical infrastructure is vastly better off, ranging from simple things like oxygen and sterile i.v. fluids, not readily available in 1918, to complex technologies such as respirators and dialysis. Should we be concerned? Sure, better safe than sorry, and concerns about publishing the sequence are worth discussing. Should we panic? No - my apologies to the fearmongers, but we will never see another 1918.

This MD hit almost all of the doubts I had: much better (and more sanitary) medical practices and supplies, the wide-spread use of antibiotics, and better general health of the populace.

But, this made me examine why there is this hysteria, and I think two points need to be raised about this. Researchers and medical doctors who study these diseases become convinced that their disease of interest is much more of a threat than any others. Be it pride, tunnel-vision, or a subconscious desire to attract more publicity or grant money to their area of research, these medical professionals have a general bias towards their particular virus or bacteria. Personally, in the two dozen virologists I have spoken too, I have seen this general propensity. I am not arguing they are wrong or corrupt, just that their dire warnings need to be considered in context.

Another factor to this hysteria concerns the general public and their view of viruses. Today the most talked about and intimidating virus, to laypeople, on the planet is HIV. A virus that people know has been around for at least two decades, is growing in total number of infections, and seems to mutate so fast that therapies become eventually useless against it and infected persons whither and die. But the comparison between HIV and avian flu is a flawed one.

When a virus, any virus, infects the body a "battle" is started between the virus transforming the infected person's biomatter into duplicates of itself and the bodies' immune system creating and mobilizing enough of the correct antibodies to combat it. If the virus wins, the immune system is decimated, secondary infections take over, and death is likely; if the body wins, the virus is generally defeated, and an immunity to that virus is set up. Avian flu falls into this model but HIV does not. The insidious nature of HIV is that it can survive the immune assault (by "hiding out" in the eyeballs) and has a high mutation rate, so the body is never rid of it.

This is where all the concern about the avian flu going through so many mutations to make it both transferable from human to human and airborne. Combine with that the previously detailed persistent nature of HIV, and you have a mental model of viral infection in the common person's mind that leads to hysteria.

Now, don't get me wrong, I am not arguing that everything will be perfectly fine, I am not that Pollyannaish, there will be infections. But, either most will recover, or few deaths will happen in segments of the population who are immune-compromised (the already ill, the elderly, the very young) or who do not have adequate access to antibiotics (the very poor). But our society has advanced to a point that these deaths will be few and far between.

If you want to talk about how to reduce even those few deaths, that is something to discuss, but we should stop the over hyping of this microorganism.

Update from Razib: Welcome Corner readers, and thanks for the link John.

The beauty of capitalism is that market niches are always being identified. You know those breast implants woman are getting, well they're so unitary in purpose just hanging there on display. Wouldn't it be better to implant an MP3 player into one breast and the music collection into the other?

Computer chips that store music could soon be built into a woman's breast implants.

One boob could hold an MP3 player and the other the person's whole music collection.

BT futurology, who have developed the idea, say it could be available within 15 years.

BT Laboratories' analyst Ian Pearson said flexible plastic electronics would sit inside the breast. A signal would be relayed to headphones, while the device would be controlled by Bluetooth using a panel on the wrist.

According to The Sun he said: "It is now very hard for me to thing of breast implants as just decorative. If a woman has something implanted permanently, it might as well do something useful."

The sensors around the body linked through the electrical impulses in the chips may also be able to warn wearers about heart murmurs, blood pressure increases, diabetes and breast cancer.

Note the less appealing secondary uses they invision.

The New York Times Magazine queries - is an inch Worth $100,000? (The Short of it). I guess that depends where it goes . . .

Down the toilet is where, apparently, according to the article, which describes the modern trend for parents and doctors to favor expensive Human Growth Hormone treatment for young boys who happen to naturally develop at the extreme left-hand side of the height bell curve – completely normal males who won’t even hit the 5 foot mark. The parents and health professionals are under the reasonable impression that height below the 2nd percentile, must provide these boys with some significant social handicaps – handicaps which could eventually affect their mental health and major life outcomes (ability to acquire mates, wages, job security, etc.). Unfortunately, attempts to empirically verify the assumptions behind this treatment have all failed:

Several years ago, around the time the Food and Drug Administration was considering the use of human growth hormone to treat extremely short but otherwise normal children, researchers were working up the results of a large-scale psychology experiment involving hundreds of middle-school and high-school students in the Buffalo area - including some who were extremely short but otherwise normal. The students didn't know the study was about height. All they knew was that each of them had been asked to be the director of a class play. They were given thumbnail sketches of various characters in the drama - "a good leader," "teases others too much," "gets picked on" and so forth - and were then asked to cast the play by selecting classmates who best fit each role.

If short stature is a ticket to social prejudice and psychological purgatory, which has been the animating idea behind expanded use of growth hormone in the last 20 years, you would have expected the shortest children in the Buffalo study to be lining up to collect their Tonys in victimhood; they would have been nominated by classmates for every beleaguered role: being picked on, behaving shyly, acting withdrawn, being left out. But that, surprisingly, was not the case. A team of psychologists, led by David E. Sandberg at the University at Buffalo, concluded that a child's stature, whether tall or small, had "minimal detectable impact" on his or her social standing among schoolmates. At least in this setting, even extremely short children (those around the first percentile) made friends and earned the respect of their peers as easily as kids of average size.

Sandberg’s evaluations have found these kids at the 1st percentile to be emotionally, socially, and behaviorally normal, something replicated by similar research in England. This isn’t a trivial find considering that typical treatment runs about $20,000 a year for 4-5 years, and typical gains are only about 1-2 inches. And yet clinical comparisons between an HGH group and a control group found:

. . . no significant differences in the quality of life between young adults who had been treated with growth hormone as children and a control group of adults (equally short as children) who had not - except that adults who had taken the drug as children had a romantic partner less often than those who hadn't used it.

So the largest scientifically verified benefit of this $100,000 treatment is less sex partners! With treatments like these, as they say, who needs sickness?

I can see why it would be tempting, even prudent, for parents to disregard such results, though. We’ve all heard the one about the taller presidential candidate, and it’s not as if the literature isn’t full of examples of the woes of shortness. Even this article admits:

There is a considerable literature suggesting that taller men receive higher pay than shorter men, and one recent study concluded that economic discrimination against short adult males was equal in magnitude to racial or gender bias in the workplace.

Right, ‘considerable literature’, so then did the paper that followed the HGH “adults� measure things like job security and wages? If it didn’t look at these kinds of things then we have a poor study design (I’d bet subjects are still too young to catch the most important variables), but if it did and didn’t find any difference, we have results that can at least fairly be regarded by concerned parents as anomalous – at odds with the larger literature. Because of a number of safe study designs, like comparing the taller of two identical twins, Steven Landsburg noted that we know height is worth about $1000 per inch per year. Sadly these substantial returns wouldn’t even match the treatment costs after an entire adulthood of working, but shortness appears to be related to more than just money – long term mental health may also suffer in important ways:

In a study of records for nearly 1.3 million Swedish men, the investigators found that for every 2 inches a man gained in height, his suicide risk dipped by 9 percent. Overall, the shortest men in the study were about twice as likely as the tallest men to commit suicide.

So we have $2000 extra dollars a year and 9% less of a chance of killing yourself. On top of this, many other studies show that inches have a significant impact on romantic outcomes, both indirectly through greater income, and directly, as increased male height is considered more attractive. Taller males have more, and more attractive, sexual partners, are less likely to be bachelors or childless, and have more children compared with others who do reproduce. A burden humorously illustrated in this unscientific ABC News pseudo-study by some very heartless, um, ‘size queens’:

� ABCNEWS put together an experiment to test just how willing women are to date shorter men . . . To see if the women would go for short guys who were successful, ABCNEWS' Lynn Sherr created extraordinary résumés for the shorter men. She told the women that the shorter men included a doctor, a best-selling author, a champion skier, a venture capitalist who'd made millions by the age of 25.

Nothing worked. The women always chose the tall men. Sherr asked whether there'd be anything she could say that would make the shortest of the men, who was 5 feet, irresistible. One of the women replied, "Maybe the only thing you could say is that the other four are murderers." Another backed her up, saying that had the taller men had a criminal record she might have been swayed to choose a shorter man. Another said she'd have considered the shorter men, if the taller men had been described as "child molesters."

So given what we know about height, it’s not totally unreasonable for parents (who probably want grandchildren) to continue to want to boost their extremely short children at great expense, despite some of these more direct studies suggesting no pay-off – at least at the time of young adulthood.

A height skeptic might wonder if any of these correlations matter in the ways we assume they do, after all “correlation isn’t causation� and the precise relationship between height and income or height and suicide may have nothing to do with height by itself. To illustrate, men who are married make more money at sales, presumably because a third skill – influencing people – gave them an advantage at both finding a partner and making more sales. Therefore just because there is a correlation between marriage and sales, doesn’t imply that giving some sales failure a wife (from your harem, in the manner of a grateful Saudi sheik) will improve his sales ability. This sheik wife may be like HGH tallness.

I am not a height skeptic, in part because the path between height and at least some male outcomes (perceived dominance/attractiveness) is not completely mysterious (see the Landsburg link for a clever experiment to find the path from height to income). Still, I can think of reasons to doubt the cost/benefit analysis in favor of HGH treatment.

Even if the drug had some measure of proven benefit, other factors, such as the possibility of untested long-term effects for new treatments, have to be weighed in these decisions. Also most families don’t have $100,000 to blow; perhaps an equal amount of money put towards good college, a decent home, or something bearing interest for this wee lad would be a wiser investment than 1 inch of height.

Related: Tall Tale, How Much Taller?, Taller ~ Richer, On Height, Medieval Height, Asian Height Gaps.

Addendum from Razib: There is book, it is called Worldwide Variation in Human Growth, and it is searchable via Amazon and Google Print. This book has tables, it reports on studies. These tables and reports transmit facts. Facts are important, and many would contend, as would I, that they should precede opinions, rather than being rendered unnecessary by the presence of an opinion. One need not read the book above, one might even make recourse to a website called google, where one can find facts. If one has an allergy to facts, or lacks the cognitive aptitude toward the manipulation and deployment of facts, one should retreat from the plain of discourse. We aren't here to play Risk, some intellectual stakes are on the table....

Labels: height

Have you ever been stuck in phone-mail hell? If you hit "0" you'll often bypass the tree, but not always. Here's a master list, published by Intuit Quickbase, covering many of the largest companies.

Just wanted to pass along some links to what will likely be a controversy when Steven Speilberg releases his film Munich later this year. The film tells the tale of an Israeli covert counter terrorist squad that was tasked with assassinating the Black September terrorists that were still at large. The tale has been told on a number of occassions, first in the book Vengeance by George Jonas. The book formed the basis for the HBO movie Sword of Gideon. Controversy has swirled around "Avner" the main character of Vengeance and many question whether he really ever was a Mossad agent. Here is one take-down published in Haaretz. Others are upset about the moralizing they fear that Speilberg is weaving into his film. The Sunday Times reports:

Spielberg has upset some by appointing a playwright (Tony Kushner) who is to the left of the Israeli left. Many Jews feel betrayed by Spielberg, but the rest of us will wait to see the film before judging.�

For an exhaustive look at the broader issue of counter terrorist actions, I'd recommend Countering Terrorism: The Israeli Response to the 1972 Munich Olympic Massacre and the Development of Independent Covert Action Teams, a Master's Thesis written by Alexander B. Calahan for his Master of Military Studies degree at the Marine Corps Command and Staff College.

Meet the Puberty Pals and your host, Paulie the Penis, as they guide you through the physical changes associated with puberty. Definitely not work-safe.

Here is the link to the Flores paper. It seems open to the public.

Update: If you can't access it, it is in gnxp forum files as "flores."

A few weeks ago I posted something titled I am a believer which disturbed some readers. Subsequently I had a conversation with Michael Vassar where he communicated to me that he thought most of science was wrong. Actually, I concurred (we both agreed physics was pretty accurate, but the action today is mostly in the bio world), and I think I hinted to this viewpoint in my post. The issue for me was not whether the hypotheses, theories and conjectures proposed by scientists were right or wrong, but that the process of science was perpetuated and facilitated, what we call 'the scientific method.' I'm not going to outline a heuristic here of how scientists go about forming hypotheses, testing them empirically and refining theories. To explore the details of how scientists do science, you can read the studies of sociologists, cognitive scientists and the essays of philosophers of science. Those of you who do science know that it is rather messy, often involving "massaging equations" and "coaxing data" and what not. Rather, I was trying to emphasize that even though the signal-to-noise ratio in science isn't very good, it is the best option we have in terms of trying to get a grapple on the world around us. Science is special. And yes, to some extent I do think scientists are a Chosen People, for ill or good.

Of course, any child has the basic minimal requisites necessary for science, the ability to form theories, some level of skepticism to prune those theories and the testing of those theories with evidence. Theories have been with us since the dawn of history, and they can be found in "primitive" tribes. People try to find evidence to confirm or reject their theories constantly. And there is a healthy skepticism that is innate in most people, that's why some are termed "gullible." But the peculiar socially mediated intersection of these traits that we find in modern science is not something that emerges felicitously out of the normal course of the daily activities of the human societies. Even though all humans have the cognitive buildings blocks that lead to science, other factors are I suspect necessary conditions to being a scientist. Today's science requires a minimal level of g. For the effort you put in (education) science usually doesn't pay. You can't chit-chat pretty ladies at cocktail parties about the new microarray technique you just perfected or your latest foray into number theory. To become a public intellectual to a large extent you have to debase and simplify your craft to a point where you become a caricature of what you truly are. On a more practical level a larger number of Ph.D.s are aimed straight for a very finite number of tenure track positions, and even most of those who do achieve tenure track positions don't really make any long term impact. A few weeks ago when I was reading American Catholic I noted a candidate for the priesthood who gave up a lucrative medical practice because he "felt the call." In some ways the religious analogy isn't totally inappropriate, what kind of adult never gives up the tendency to ask questions that don't relate to their personal life or financial security? What kind of adult spends 70-80 hours breeding flies, running simulations and derivings proofs rather than spending time with their families, watching sports or going to church?

But the individual characteristics of the proto-scientists, those who are a subset of the broader human species, is not enough. I think it can be reasonably argued that science as we understand it has been a one off invention. The ancient Greeks came close, but the pre-Socratics gave way to more explicit streams of ethical and metaphysical philosophers and technicians like Archimedes or Hero. Science needs a particular social context, and a scientific culture. The Lunar Society was simply an illustration of the general concept. It would be an oversimplification that children can't do science because they don't have journals, conferences and standard units of measurement, but that is certainly part of it. It is commonly held that only humans can generate culture, learning and improving on what we learn from conspecifics. Our culture has been on an ascending ratchet upward in complexity for millions of years now. But many aspects seem to me to be ahistorical. Religion for example is I think one of those. I've said before that if you set loose a bunch of amnesiacs on an island they would create a supernatural world-view soon enough. While children have the basic tools of science, it is a unintuitive social complex which they can not generate with ease. In contrast, I believe religion is "closer to the cognitive code" so to speak, like art, language or basic social pecking orders it emerges naturally, is evoked, from any random collection of human beings. Technology is something we associate with science, but some historians would make the argument that up until about 100 years ago technology was a matter of tinkering and testing by artisans and hobbiests, not a matter of implementation of scientific modeling. Certainly H. erectus had technology, but the stability of the Oldowan Culture does not seem to indicate too much innovation, and certainly doesn't resemble the explosive ladder of complexity and Mooresian geometrical rate of growth that is the characteristic of modern technological civilization driven by pure science at its root.

Humans can thread many strands into the edifice we term "culture," but some are intuitive, natural and "closer to the cognitive code." If the great French culinary tradition died tomorrow, in a century I suspect someone would taste those fine tastes again. If every systematic theologian was snatched from the earth by the hand of God, within a few generations systematic theology would reappear. But if every scientist disappeared from the face of the earth (engineers inclusive), then I believe civilization would collapse, after the lawyers had sued every company and individual who they could hold liable. If every biologist disappeared I believe the hole in science could be closed within a generation. As long as enough of the culture survived the fire would remain lit in the demon haunted world, but if the individuals who perpetuated the scientific culture disappeared it would become a thing of myth within a generation as civilization degenerated back into "gunpowder empires." And the culture is all in the end because it is necessary, the last step on the long journey. Psychologists like Kahneman and Tversky show us that scientists are generally biased, ignorant and intuitionally blinded individuals. For a specific example, consider the debate between the "Classical" and "Balance" schools of evolutionary genetics, they spent 30 years debating whether one or the other was right. When Lewontin and Hubby came out with their paper showing enormous levels of polymorphism the two "orthodox" rival theories were both rendered outmoded. Neutral Theory rose up to explain the high levels of polymorphism, and the proponents of the two older theories integrated the new data into their paradigms (many, like Richard Dawkins, quietly accepted defeat but declared they'd won!). Nature is always more clever than scientists, they are always catching up to her tricks after she's poked them in the ribs and run off.

So I suggested above that science and religion are very different, which to some extent seems to fall into line with S.J. Gould's Nonoverlapping Magisteria concept, which can be set against the war between science and religion. Like most things the truth is in the middle, it seems quite clear to me that some religious ideologues do think that their religion explains everything under the sun and the stars. On the other hand, I also tend to agree with cognitive scientists that no matter what religionists profess, in their heart of hearts they all worship the same supernatural agent(s) in the sky, which are really only glorified Faces in the Clouds. But there is a crucial difference between science and religion in that I believe that the former is contingent upon a particular culture, while the latter is universal. Which is why I used the allusions to Jews in my previous post, though I could have also made an analogy with the Roman Catholic Church, when it came to the camp of science. Specific world religions are highly institutionalized and often formalized, and like science they are contingent on cultur and history. The Jews have survived 2,500 years as a coherent ethno-religious group. The Roman Catholic Church is an institution that can date itself back to European antiquity. Religious organizations are powerful macrosocial entities, they are often powers who can shape their own destiny and hold their own against the powers that be. Like it or not scientists live in a world of esoterica, and non-scientists are going to be the ones who will fund them and sponsor them. A true scientific culture isn't really more than two centuries old. Who knows how long it can last?

Now, the truth is that I don't think it will have to last that long. I suspect that the end of technological civilization is near, within the next century or two (if that), either via sociologically induced collapse (i.e.; our cognitive software and biological hardware simply becomes too maladapted for our technological prowess and we immolate ourselves) or toward some sort of technological singularity. The key is that scientists are going to be necessary players in the generation of the singularity. Scientists don't have to preserve their institutions and culture for more than a few centuries. So there you have it. I think the stakes are high, high enough that I stooped to using religious language and somewhat unhinged rhetoric. Dare I say, my science, right or wrong?

You don't have to be mad to be a parent, but it helps. This is certainly not an original thought but it's a truism nonetheless. Recent research is aiming to expand our insight into how parental behavior changes when children are introduced into their lives. Dr. James Leckman of the Yale University School of Medicine offers a tantalizing glimpse of his recent research into Obsessive-Compulsive Disorder:

His plan was to hunt down the neurotransmitter that might hold the key to OCD, in the same way that the neurotransmitter serotonin plays a role in depression. He did chemical analyses of the cerebrospinal fluid from OCD sufferers and found . . . nothing.

Rather than leave the samples languishing in the freezer, Leckman sent them off to another researcher to check for less well-known chemicals. “The guy who examined them was amazed by the levels of oxytocin,� Leckman says. Oxytocin is the hormone that tightens the parent-child bond. Knock out the oxytocin gene in female mice, and they lose the ability to nurse their young. Inject oxytocin into animals, and they show grooming behaviour and an increased faithfulness to one mate.

“The question was,� Leckman says, “what did all the behaviours associated with oxytocin, such as pair-bonding, have to do with OCD? Then I remembered how I behaved when my wife was pregnant with our first child. Every time she got a fever or a cold, I had these intrusive thoughts about harm coming to the baby. I remember my wife cleaning all the time, even moving the refrigerator. And even though I was a really busy medic, I found the time to build a cradle from scratch. I just came up with the idea that [parenting] is a normal, adaptive version of OCD.�

Leckman suggests that, given the high rates of infant mortality during human evolution, parents whose brains contained the neurocircuitry of paranoia would be most successful at keeping their offspring alive. When these circuits are switched on at the wrong time, he theorises, the obsessive behaviours become problematic and result in OCD. In particular, two variants of OCD — compulsive checking to ensure no harm comes to one’s family and an inordinate desire for cleanliness — are familiar to new parents.

Most recently, Leckman has questioned expectant parents and new parents on their feelings about their babies, using a method similar to that employed to diagnose OCD. He has found that just before and just after the birth the feelings and fears of both mothers and fathers are strikingly reminiscent of those voiced by OCD sufferers. He is keeping the exact results under wraps, and is preparing a paper for publication. Interestingly, Donald Winnicott, the late English psychoanalyst, commented in 1956 that, in order to relate to their infants, mothers develop a heightened sensitivity that is “almost an illness�.

Since we've talked about height on this blog before, I thought the following might interest some...from The Aegean Bronze Age:

All the large samples have produced very similar averages of height...around 1.67 m [about 5'6] for men and 1.55 m [about 5'1] for women, but with a range that in both sexes spreads over 20 cm [a little under 8 inches] around the average...these averages are only half a centimeter lower than in modern Greece....

I don't know if the average for modern Greece is correct, the book dates from 1994, and many works of scholarship often use old data when drawing upon facts from outside of their discipline. Here are height tables for Greek boys and girls, even assuming that Athenians are taller (for whatever reason) than average the comparison to modern (21st century) Greeks is off. But, the legends of tiny ancients go back at least few centuries, so it doesn't exculpate scholars totally.

Here is some more from Mycenaeans:

...The skeletons of aristocrats in Grave Circle B show that the women were 1.58-1.61 [5'2-5'3] tall and the men were 1.61-1.76 m [5'3-5'9] tall, around 6 cm [2.4 inches] taller than commoners.
...
Zeta 59 [remains of an individual] was also a big man...he was 1.75 m tall [5'9].
...
Gamma 55 was another big man, 1.76 m tall....

These might not be giants on the march, but they are certainly more substantial than the 5'0 tall roman rankers described to me by one anthropologist. Certainly peasant farmers and (later) urban poor recruits are not necessarily equivalent to aristocratic warriors 1,000 years before their time, but, it suggests that one should take gee-whiz generalizations with a grain of salt.

Labels: height

This isn't big news, but confirmation of a somewhat amusing trend, Emergence of Young Human Genes after a Burst of Retroposition in Primates:

...We estimate that at least one new retrogene per million years emerged on the human lineage during the past ∼63 million years of primate evolution. Detailed analysis of a subset of the data shows that the majority of retrogenes are specifically expressed in testis, whereas their parental genes show broad expression patterns. Consistently, most retrogenes evolved functional roles in spermatogenesis...We conclude that retroduplication significantly contributed to the formation of recent human genes and that most new retrogenes were progressively recruited during primate evolution by natural and/or sexual selection to enhance male germline function.

What sort of phenotypic changes would affect fitness (differential reproduction), ergo, respond to selection? You don't have to look too high for a trait that might stick to those specifications.

Related: Sperm competition. Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity.

Some of you might know that Robert Jordan came out with Book 11 of The Wheel of Time today. There are only a few reviews up, and they are mildly positive. I'm waiting for the harsh press though, I only went up to the first few hundred pages of book 7 years ago.... Anyway, some of you also know that a real author is coming out with a sequel worth waiting for in about a month.

Update: First negative review on Amazon is up!

IT is clear that RJ has hired someone to write positive reviews for this book. Many were posted here before the book went on sale, which shows that TOR and AMAZON know that they'll never sell this junk without cheating. I've read this book. It stinks. Here's why:

Once AGAIN RJ delivers junk. Rand is AGAIN MIA for most of this book. When he appears, it's only to be whiny and annoying for a short time. There's more on Mat here--which is NOT a good thing. Once AGAIN the Aes Sedai are skirt-smoothing, icy-staring, sniffing, scowling, tea-drinking bosomy witches. Once AGAIN RJ's chapters meander into the realm of FILLER and once AGAIN the ending is a quick burst of unbelievable garbage that makes little to no sense.

Jordan says that his female characters take at least one trait from his wife. If the characters are a mirror upon her she must be a vapid bitch.

Update II: A real life Lord Frey? Here is a recent family photo.

Carl posts about the new Hobbit finds. John has a short comment (more tomorrow says he).

Update: John's update is up.

(Jason Malloy provided this interesting link in the GNXP Forum)

Smarter on Drugs

“Just as Ritalin can improve the academic performance of hyperactive children, it can do the same for normal children. It is commonly thought to boost SAT scores by more than 100 points, for both the hyperactive and the normal user. Many healthy young people now use it that way for that purpose, and quite frankly, there is no stopping this abuse.�

I found this claim interesting. I don’t have the background or knowledge to evaluate it. Hopefully knowledgeable readers will comment.

Up to 5% of males are diagnosed as having ADHD. Many schools require medication for kids diagnosed as having ADHD. Wouldn’t a 100-point boost in SAT scores show up in national test scores? Is there any study that backs up the author’s claim?

Note that 100 SAT points is equivalent to about 7 IQ points. But even if the 100-point claim is valid that doesn’t mean that Ritalin is increasing IQ. E.g., vocabulary test correlate highly with IQ tests. But having access to an online dictionary that significantly improved one’s performance on a vocabulary test wouldn’t increase a person’s IQ. It would just break the connection between tested vocabulary and IQ. Likewise Ritalin might increase the ability to focus and so increase test performance but that increased performance might not reflect increased “g�.

(Many abilities correlate with “g�. As biotech improves so that specific abilities can be enhanced, it is not clear to me that “g� is being increased. The science of measuring “g� will have to adapt to advancing brain tech.)


This article says that under long-term treatment with Ritalin, ADHD children showed a 2.5 point increase in total IQ. Other articles claim there is no improvement in IQ (In fact some articles claim that if used too early, Ritalin can hinder proper brain development.)

(I would like an online resource that numerically documented the mental effects of substances such as caffeine and Ritalin.)

From wild wolf to domestic dog: gene expression changes in the brain:

Despite the relatively recent divergence time between domestic dogs (Canis familiaris) and gray wolves (Canis lupus), the two species show remarkable behavioral differences. Since dogs and wolves are nearly identical at the level of DNA sequence, we hypothesize that the two species may differ in patterns of gene expression...Our results suggest that strong selection on dogs for behavior during domestication may have resulted in modifications of mRNA expression patterns in a few hypothalamic genes with multiple functions. This study indicates that rapid changes in brain gene expression may not be exclusive to the development of human brains. Instead, they may provide a common mechanism for rapid adaptive changes during speciation, particularly in cases that present strong selective pressures on behavioral characters.

It is interesting to note that Nazi-sympathizing scientist¹ Konrad Lorenz (co-inventor of modern ethology along with Nikko Timbergen) actually extrapolated from animals to humans in warning about the dangers of "domestication." My recollection is the average wolf is more intelligent than the average domestic dog, though I am would not be surprised if the variation within dogs is great enough that border collies are brighter than the wolves that it was bred to keep an eye on.

1 - Anyone who doubts the label "Nazi-sympathizing" should read The Ape and the Sushi Master, Frans de Waals' series of essays about primatology and ethology where Lorenz's history is detailed, though Waals is clearly sympathetic to the doyen of his profession and tries to make a good show of apologia via some hand waving.

This post is really just a short addendum to David's post. He offered that perhaps there are 5 loci that control skin color in humans. Well, it's more complicated than that I suspect, but let's assume there are 6 loci. I'm going to present a super simple model to illustrate what I think is part of the reason that the inheritance of this trait contradicts some of the high school biology most people learn, which tends to emphasize simple Mendelian traits which are explained in the dominant-recessive paradigm.¹

OK, so, as I said, we have 6 loci which control the expression of the skin color phenotype (basically a proxy for the density of melanocytes). Now, to make things simple, assume there are two alleles, or flavors, at each locus. At all the loci the alleles are either "on" or "off," so you can have a profile at a locus of AA (both on), aa (both off), or Aa (one of each). Though the details of the sequence of each allele at each locus is no doubt different, assume they all have the same phenotypic effect of equivalent "dosage," let's call it "one dosage unit" (1 d.u.). In other words, someone who has all 12 alleles "on" would have 12 d.u. of melanin expression, someone with them all "off" would have 0 d.u. of expression. We are neglecting any interactional effects, so assume pure additivity and independence.

Now, assume you have two parents with the genetic profiles as follows:

Parent 1 (P1) Aa, Bb, Cc, Dd, Ee, Ff.
Parent 2 (P2) Aa, Bb, Cc, Dd, Ee, Ff.

In other words, they have the exact same profiles, and they are expression 6 d.u. of melanin, since at each locus they have an "on" and "off" allele. On visual inspection both would be "brown." A parent with 0 du expression would be "white," and 12 d.u. expression would be "black."

Long time readers know where I'm going with this, but bear with me. What kind of children would they have? Each of the children would have 6 loci, with 2 alleles, one from each parent. So, you would have:

Child P1P2, P1P2, P1P2, P1P2, P1P2, P1P2.

Each slot would be filled by one of the two alleles at the equivalent locus from the parent. Note that I rigged it so that the expectation would follow a binomial distribution like a coin flip, each slot has a 50:50 shot as being filled up by an "on" or "off" allele, because the parents are heterozygous at each locus.

The expectation is that the child would have a profile just like the parents, but, the number of loci being sampled during random assortment and segregation is pretty small.

Expectation (X) = np, where n ~ trials (the total number of slots on all 6 loci, 12) and p ~ 0.5 (the chance of either an "on" or an "off" result in this case). So, expectation (X) = 12*0.5, or 6, ergo, 6 d.u.s expectation of expression, just like the parents. This fits our intuition well.

But what about the variance? Variance (X) = np(1 - p), or, variance (X) = 12*0.5(1 - 0.5) = 3. Since a standard deviation is the square root of the variance (let's keep it in intelligible units), you get an expected deviation of 1.73 d.u.s during each round of successful reproduction. There is only about a 1 out of 4 chance that a child will be exactly at exactly 6 d.u.s. There is a 1 out of 14 chance that the child will express 3 or fewer d.u.s, and an equivalent probability that the child will express 9 or more d.u.s. If one assumes that these extremes verge toward the "white" and "black" phenotypes, one could say that there is a 1 out of 7 chance that each time these "brown" parents have a child, it will not be brown. This neglects the variation between 4 and 8 d.u.s, which would likely be discernable to visual inspection (quick back-of-excel, I figure that if the parents above have 6 children, there will be a 60% chance that at least 1 will not be brown as defined by a 4-8 d.u. range of phenotype).

As I stipulated above, I rigged the scenario for ease of exposition. The parents could both be brown, but be homozygous on all the same loci (P1 = AA, BB, CC, ee, dd, ff, P2 = AA, BB, CC, ee, dd, ff) which would result in no variation in the children if the trait was totally heritable in a conventional genetic sense (i.e.; no epigenetic factors, developmental randomness, environmental component of variation, etc.). Or, the parents could exhibit different genetic profiles, in which case the simplicity of expectation and variance wouldn't be so easy to determine. This neglects the almost sure reality that 1) loci will have different dosage effects, 2) there will be some interactional aspect 3) some of the loci will be wide-ranging in their regulatory functions (like MC1R).

The only moral is one should go beyond the Punnett Square abstraction where phenotypes have simple (monogenic) causes.

Update: This applies to eye color as well, as I talked to an individual who claimed that their father had brown eyes, and mother green eyes, while they have blue eyes (and seemed sure of paternity based on other resemblences). One could imagine a scenario where the sampling process resulted in this individual getting a disproportionate number of "fair" alleles from both parents, which resulted in the expression of a phenotype that looks "blue" to the naked eye. Imagine, for example, that the 50% of the father's alleles are "blue," and 75% of the mother's, one could selectively sample out of that (since 1/2 of the alleles come from each parent) fraction to generate a frequency of blue alleles greater than 75% (the mother's phenotype being determined by the 3 to 1 blue to brown ratio, so a 'true blue' phenotype would need to be greater than that).

1 - I think terms like incomplete dominance and codominance are pretty confusing, because they take the dominance-recessive dichotomy as an important reference that makes the rest of genetics intelligible. In reality, I think it just adds a conceptual overhead which isn't justifiable in the post-genomic age. I also think penetrance is not really worth it as a term, not to mention that it sounds kind of dirty in our sexualized age.

Anyone with an interest in human genetics will occasionally be amused or annoyed at the treatment of genetics in films and TV. I will give my own Oscar (TM) nomination for the worst genetic mistake in the movies, but readers may have other candidates.

I am not thinking so much of movies like Gattaca with a specific genetic theme, as of the general disregard for genetics shown in casting and storylines. For example, I recall a film where a male character was said to have an identical twin sister. [Note 1]

On a more mundane level, we often see blue-eyed screen couples with brown-eyed children, siblings of wildly different height or features, and other genetic improbabilities. You might think that casting directors would at least make sure that the actors were of the right racial origins for the characters, but even this is often ignored. I recall a British TV series where a Mexican character was played by a South Asian, and now on Lost we have an Iraqi played by an Anglo-Indian [Note 2]. But this probably doesn't matter to most Western viewers (myself included) as all brown dudes look much the same to us! :-)

There is a similar looseness in the casting of black (African-American) characters. Remember the Cosby Show, where the five children ranged in colour from dark chocolate to nearly white, with two of the children much lighter than either of their parents? This is not quite impossible, but if I were Dr Huxtable I would demand a paternity test.

I don't find any of this too distracting unless it is significant to the plot. It is more of a problem where the casting makes some key element of the plot genetically incredible. For example there are several movies where a character with black ancestry is 'passing for white'. For credibility the actor needs to be a borderline case: not Wasp-white, but not obviously black either. The classic weepie Imitation of Life was plausible from this point of view, as was a 1950s British film called Sapphire. But Anthony Hopkins (in The Human Stain) is not a suitable choice as someone passing for white! Then there was a film where Robert Duvall, playing a Southern redneck white, discovers that his biological mother was black. Oh, please! It would be credible if he discovered a black great-grandparent, or at a pinch even a grandparent, but not his mother. The opposite situation arose in Mike Leigh's Secrets and Lies, where an adopted black woman, tracing her natural parents, discovers to her shock that her mother is white. The casting of this role is tricky: it needs to be someone black enough not to suspect their mixed ancestry (which in England is hardly a rarity), but not so black that it is incredible. There may be actresses who meet this specification, but Marianne Jean-Baptiste is not one of them. She is just too black to have a white mother, especially a pale redhead like Brenda Blethyn. For me, at least, this genetic implausibility wrecks the central element of the plot.

But my Oscar nomination for most disastrous genetic blunder in the movies (and the case which prompted me to write this post) has nothing to do with race. It comes in a recent film called Tiptoes.


...
This apparently had a limited cinema release last year, but is now available on DVD. I must admit my main reason for watching it is that it features Kate Beckinsale, and I would watch almost anything with Kate in it. (Though I may draw the line at the Underworld sequel. I sympathise with the critic who said he would rather stick needles in his eyes than watch Underworld again.)

Tiptoes is about a young woman artist (Beckinsale) who is engaged to a tall, hunky firefighter (Matthew McConaughey). So she is shocked when she discovers that most of his family are dwarfs, including his parents and his twin brother (played by Gary Oldman with kneepads). The rest of the film explores her reactions as she gets to know the family and the wider dwarf community, and the resulting tensions between her and McConaughey.

Of course, there is nothing impossible about two achondroplasic dwarfs (as the parents seem to be) having a non-dwarf child, though I rather doubt that a dwarf woman could bring twins safely to term. The problem comes with another major part of the plot. Shortly before she discovers McConaughey's family secret Beckinsale has learned that she is pregnant. Naturally she is worried that the baby might be a dwarf. So does McConaughey reassure her that the chances are minuscule? No, he says it is 'definitely possible'. And she goes on to consult various other people, including a dwarf doctor, all of whom solemnly warn her that it is quite likely. And to cap it all, when the baby is born, it is a dwarf!

Whatever were they thinking? The most common forms of dwarfism are due to a dominant gene defect. A non-dwarf (like McConaughey) would therefore not have the relevant gene, and would be at no more risk of having a dwarf baby than anyone else. It is true that some rare forms of dwarfism are due to recessive gene defects, but in this case McConaughey's dwarf parents would be homozygous, and McConaughey would himself be a dwarf. [Note 3] Either way, the storyline seems genetically absurd. Maybe there is some rare form of dwarfism in which the defect is dominant (in the sense that it can be expressed in the heterozygote) but unpredictable in its effects, so that the bearers of the gene may be either dwarf or non-dwarf. If so, I stand corrected. But even in this case the film would be seriously misleading, as it gives quite the wrong impression about dwarfism in general. Were the writers and director simply ignorant of the genetic facts, or did they deliberately ignore them for the sake of a more dramatic storyline? If the latter, they are doubly culpable, as one of the aims of the film is to dispel prejudices and misunderstandings about 'little people'. The average viewer will draw the false conclusion that it is never safe to have children with any relative of a dwarf.

But don't let this put you off watching it! Genetics apart, it's an unusual and surprisingly enjoyable film with good performances from the leads (especially Oldman) and a large cast of small supporting players. It ends abruptly with Beckinsale breaking up with McConaughey, and on the brink of a romance with Oldman. Apparently the director (Matthew Bright, who made the cult classic Freeway with a young Reese Witherspoon), wanted the outcome to be more explicit, but the financial backers vetoed this and took control of the final cut. The world is not yet ready for dwarf-on-Beckinsale action.

Note 1. There is in fact at least one recorded case where MZ twins developed as a boy and a girl, because one twin from an XY zygote lost its Y chromosome at an early cell division, and grew up as an XO female, while the other twin was a normal XY male. But this is exceedingly rare, and I'm sure it is not what the scriptwriter had in mind.

Note 2. According to an interview, Naveen Andrews 'grew up in Wandsworth [London] with his brother and parents, Nirmala and Stanley, who moved from Kerala [South India] to London after their arranged marriage in 1965.' If 'Andrews' is their original family name, this suggests that his parents are Anglo-Indians in the sense of being from a community of mixed British and Indian ancestry. In the 19th century it was common for the lower ranks of the British military and commercial classes in India to marry Indian women, who would convert to Christianity. Their offspring could not easily marry either British or Indian partners, and therefore became a distinct endogamous community, with occupations mainly in the railways and public services. Anglo-Indians in this sense should be distinguished from the offspring of mixed Anglo-Indian marriages in Britain today. There is also an older usage of 'Anglo-Indian', used to describe the higher levels of British society in India under the Raj. In this sense the term is analogous to 'Anglo-Irish', and does not imply any Indian ancestry. Intermarriage at the higher levels of society was rare after the 18th century. This old usage can cause misunderstanding when people like Rudyard Kipling or Augustus De Morgan, whose ancestry was entirely European, are described as 'Anglo-Indian'.

Note 3. In principle one dwarf parent might be heterozygous for a dominant condition, such as achondroplasia, while the other is homozygous for a different recesssive condition. An offspring (like McConaughey) might then be a non-dwarf but carry one recessive dwarf gene. But in this case there would no additional risk to his children unless his partner also carried the recessive gene, which is highly unlikely.

In the gnxp forum files I've put a PDF of a Nature Reviews Genetics article titled "The applications of behavorial genetics outpacing the science?" under the name "behaviorgen."

An interesting article here in today's London Times about some research on the evolutionary psychology of hoarding. I may comment further when I've seen the full research.

Update from Razib: The paper is in GNXP forum files as "endowment."

You might have encountered the Trolley problem:

A trolley is running out of control down a track. In its path are 5 people who have been tied to the track by a mad philosopher. Fortunately, you can flip a switch which will lead the trolley down a different track. Unfortunately, there is a single person tied to that track. Should you flip the switch?

It seems obvious to most people that you should. (Don't fret if you disagree -- so do I.) But what if we change the scenario:

As before, a trolley is hurtling down a track towards five people. You are on a bridge under which it will pass, and you can stop it by dropping a heavy weight in front of it. As it happens, there is a very fat man next to you - your only way to stop the trolley is to push him over the bridge and onto the track, killing him to save five. Should you proceed?

Polls find that most people think this is not permissible. Indeed, the high degree of agreement among people's intuitions about these problems has led to the speculation that they may be revealing the facets of an intuitive morality instinct/module/faculty.

Now consider this (related) item from the recent pol poll: "The life of one American is worth the lives of several foreigners." Operationally, we tend to act as if this were our belief. However, you may (like me) find this to be an uncomfortable admission. (If you don't, perhaps the graphic images in Nick Gillespie's latest piece in Reason will change your mind [warning: graphic image].) Philosopher Peter Singer has done work on this subject. He offers a "Cosmopolitan" utilitarian ethic, which I don't find compelling enough.

Update: Good comments. BTW -- Bryan Caplan's comments on Ethics and IQ is what sparked this musing about moral intutions. In particular, Caplan claims that "One of our most basic moral intuitions is that people who succeed because of their personal ability deserve what they have." Sure about that?

Update 2: From the comments: an article by Carl Zimmer that details this topic.

Over at Sepia Mutiny Abhi points me to this piece titled Transnational marriage and the formation of Ghettoes. Here some data from Britain:

% marrying spouse from Indian subcontinent

Pakistani male - 48%
Pakistani female - 40%
Bangladeshi male - 60%
Bangladeshi female - 40%
Indian men - 38%
Indian women - 15%

I'm not going to comment much further, except to point out that considerations of the negative impact on the society at large from the emergence of ghettos is a real issue, but it also often neglects the impact that a particular social matrix has upon individuals who are not of their own choice born into a particular community (for example, girls born into a community that still maintains the immigrant ethos and where a large number of foreign born women recapitulate norms and patterns atypical for the West and so impart to their son certain expectations of what a "good wife" is).

Rather, I'll sketch out the emergence of the "love marriage" as narrated in a short book titled Marriage, a History, by Stephanie Coontz, that I read a few weeks ago. The author is a historian, and so she brings particular biases to her work. For example, her view of evolutionary or innate biases seems to be oriented toward an assumption that Evolutionary Psychology^TM is the only paradigm, which once falsified in a strong typological form obviates the need to take into account biologically controlled cognitive biases. The author might have benefited from the contrasting takes on male-female relations viewed through an evolutionary lens in The Mating Mind (weak pair bonds, operational polygyny) and The Ancestress Hypothesis (deep time history for marriage, monogamy and strong pair bonds). I will stipulate that I generally am very skeptical of the idea that phenotypic monomorphism is the norm on many psychological traits relevant to culture, and I am convinced that there are multiple social "fitness peaks," and there are likely different cultural and individual ESSs. The genetics can't resolve this issue yet as to what man's nature is yet, that's for sure.

The author's basic contention is that the modern pair bonded love marriage as the center of social organization is a relatively new thing, and emerged in the Western world as paramount in the 20th (and late 19th) century after a long period of evolution, beginning in the medieval period. One interesting point the author brings up is that the bars on marriage due to incest were extremely high in Western Europe because of the Roman Catholic Church. Prior to 1300 the incest bar extended to 7 degrees of relation (dropped to 4), and was expanded to include relatives of God parents and a host of other non-blood quasi-kin associates. The author offers that this was convenient in the case where the Church was brought in as an arbiter in elite marriages, it was leverage used against elites so that favors could be traded in return for ubiquitous dispensations. The fact is that for a period it was almost impossible for the European nobility to marry someone who they were not related to in some fashion, literally, or symbolically. A few years ago Adam Bellow wrote a book, In Praise of Nepotism, where he argued that the Roman Catholic Church's campaign against "incest" and adoption was in part motivated by the fact that if a wealthy man or woman died without heirs (nephews and nieces could not inherit) their assets would often be given to the Church. This materialist argument might not be absolutely correct, but it is I think at least on the right track and almost certainly a component of the full explanatory vector. The same dynamic was not as strong in Eastern Europe, where the Christian churches (at least until the Ottoman period) were not as powerful as corporate entities with temporal interests (recall that starting in the medieval period the Pope was also an Italian "Prince"). Additionally, for reasons not stipulated, in Southern Europe many of the aspects of Church teaching were not enforced to the same extent or in the same fashion, so the special factors do not apply to the same extent (one thing to remember is that Northern European kingdoms tended to need more Christian legitimacy during the early medieval period because of pervasive pagan relicts or a recent pagan past).

As a byproduct of the Catholic Church's hold on marriage as a sacrament, in Western Europe it was often relatively easy to get married (mutual consent, or reported consent!) and extremely difficult to get divorced. Paradoxically, this resulted in the strengthening of pair bonds, because people only got "one shot" officially (for wealthy men who wanted heirs this was important, bastards were eventually excluded from any rights). Of course, annulments could mitigate this risk, but the Church at different periods had different attitudes toward the ease of this escape hatch. Additionally, convents and monastic communities often absorbed many individuals who did not, or could not, get married. The discouragement of incest resulted in a nobility whose social networks were spread out, and weakened the interests of clan-and-patrilineage. Non-kin associations (guilds, etc.) were pervasive and powerful.

As the modern period dawned and the Reformation destroyed the "old order" a new system emerged where romantic love between equals began to be emphasized to an even greater extent and celibacy was less of an option (the convents and monasteries were closed in Protestant countries). At first the relationship was rather pragmatic, as couples often married explicitly toward the interests of pooling resources and generating enough start up capital to fund a business or buy a parcel of land. The weakness of extended families and kin networks meant that the non-wealthy commoners often moved out of their parents' homes and started their own househould. This pushed back the age of marriage (in other societies the start up capital needs were lower since parents and the extended family operated as a sort of distributed support system for young couples). During the 19th century the rise of "rights" and female liberation (in starts and fits) resulted in a shift of male attention toward the family and his wife as the primary relationship in his life. Before socialization with male companions and subordinates had been an important factor, but over time "family life" and the separation between the public and personal became more explicit.

To truncate the narrative, we have a situation where in the early 21st century the "Western" concept of a love marriage aimed toward individual fulfillment is the dominant media paradigm. There is a perception that arranged marriage societies are in an "earlier" stage of development. I don't think this is correct. Coontz points to the relative lack of jealousy in some South American tribes as regards pair bonded fidelity as evidence that there isn't hard-wiring toward behavioral scripts on this level. I think she misreads the situation. As I note above, her implicit assumption is that there is a Ideal System of Marriage, or, there are a host of historically contingent social systems exploring "culture space." I think where Coontz gets this wrong is that she neglects that the different social arrangments might be alternative equilibriums across the culture space, and that many variants are disfavored, or at least unstable over the long term.

Consider benzene, the ubiquitous six-carbon molecule which comes in two primary structural states, boat and chair conformations. The geometries that molecules are stable at are contingent upon the characteristics of the molecule as a function of structural implications implied by its lower order subcomponents (the atoms with their bonds created by overlapping electron valence shells). A particular conformation has implications in terms of the properties of the molecule, and the most common conformations tend to be those at lower energy states. One can scaffold the situation in a fashion so that unlikely states can arise, for example, from what I recall buckyballs can trap inert gases and so create peculiar assocations that are normally disfavored.

Back to marriage, and culture, my point is that formalized polyandry might not be common, but, it does occur given the appropriate inputs (in poor regions like Tibet a band of brothers will marry one woman because that way they can pool their resources together and set up a household). Similarly, there is a wide range in terms of propensity to pair bond across cultures and individuals. Variation does not refute a contention that there are particular expectations, biases or correlations that can be attributed to a particular behavioral phenomenon. Across the "civilized" cultures of Eurasia there is an expectation one might have in terms of the particular form of marriage that is the norm, powerful patrilineages (and the pater familias) often call the shots in terms of important life decisions for those who are in their charge. In contrast, the Western "love marriage" is more free form and characterized by a flux dictated by the needs of each individual. Coontz's narrative history shows how modern marriage is the byproduct of a "boxing in" process where the Roman Catholic Church transmitted to the barbarian post-Roman polities some of its romanitas in exchange for a monopoly on the arbitration of particular aspects of the life of the elite. Over time, the peasantry also shifted from common law marriages to sacramentalized marriages, and the particular needs of the Church, which Bellow articulates in a materialistic paradigm and Coontz implies in her argument, canalized the evolution of society toward a more individualistic pair bonded structure. To borrow an analogy from evolution, the Church was a background condition which induced particular selection pressures on the memes circulating through the society. Once the societial norms managed to "peak shift" across the valley of death (driven by the tight marriage strictures of the Church) which separates the arranged marriage-joint family structures of the Eurasian civilizations toward the individualistic love marriages that are the norm today, we reached a new fitness equilibrium. The unleashing of modernity as a whole via the explosion of the West is I think driving the world across the low societal fitness valley (in part because modern technology and consumer society alters the background pressures and shifts the fitness landscape on its head).

But why do people enter into love marriages in the first place? This is where Geoffrey Miller's ideas come into play, he argues that loose short-term pair bonds were the ancient norm. I'm skeptical as to his whole thesis on this issue (see David's review), but there is compelling biological evidence that "love is natural," at least in some form. Even societies where arranged marriages are the norm have myths and fables which allude to love marriages, and its persistent draw. I have argued before that in some ways the culture of the modern West is a throwback to pre-Neolithic times, when smaller scale societies were dominant, and powerful super- patrilineages which logically led to the creation of top-down authoritarian states were likely not as pervasive a factor in human life. So, one reason that there is a fitness peak for marriages with a strong pair bond is because I think they are more "natural" in some ways than the arranged marriages that were common in "advanced" civilizations (where the pair bond was enforced in terms of sexual fidelity on the part of the woman, but was psychologically weak for both male and female). The relative distance of North Indian men, or ancient Athenians, or traditional Chinese men from their wives and association with patrilineages or male social clubs might be excessive in terms of what our psychology is outfitted for. In the context of the inputs and influences of the mass society around them it was a natural tendency of the cultural median because centralization of power and decision making was the norm, and strong husband-wife relations might have diminished the succcess of males in the patrilineage molded rat race. With the decentralization of power, the rise of republican deomcracies, and economic productivity freeing people from want and the need to pool resources and draw from parental-communal capital, it makes sense to me that individuals would begin to opt out of familially dictated marriages. They are doing what comes naturally.

In short, there are many ways to arrange a society, but the options are stable only with certain preconditions (and those preconditions vary). Biology is important because it leads to a psychology which is amenable only to a finite number of concepts and arrangements, though there is variation around the median. Additionally, the background conditions are always shifting as culture evolves in a complex feedback loop onto itself, always working with the same basic cognitive units as foundations (though those cognitive units vary from person to person, and, perhaps population). Interestingly, there are theorists who argue that sex evolved over time via a step wise process where the changes were structually favored only in one direction, ergo, multicelluar complex organisms are "boxed" in by their evolutionary history and by the fact that selection has only a narrow window of consideration (I am skeptical of this theory, bdelloids are asexual). Similarly, the particular historical contingencies which led to the rise of the Western love marriage might now be irreversible, even though they were unlikely in the first place (at least as any particular time).

Addendum: Coontz points out that Ireland was subject to a peculiar lag in terms of marriage norms in relation to the rest of the Western Europe. When divorce was banished from most of the Catholic world, in Ireland it was a common feature of life. When divorce was once more common in the rest of the West, Ireland remained tied to older Roman Catholic norms. Similarly, the demographic transition and rise in age of marriage that occurred with the transition toward a more "modern" economy was not to be found in Ireland until the 19th century. But, during this period a revived Roman Catholic Church campaigned for a social transformation which resulted in sharp increases in the age of marriage and a rise in the number of life long singles who were absorbed by convents or remained bachelor uncles. The speed at which this occurred is chronicled in the second chapter of American Catholic. Similarly, there was a sharp drop in the age of marriage throught the West in the 1950s, as men and women were marrying earlier than they had for many centuries (the age of first marriage is now back up of course).

“Are there large numbers of covertly “fascistic� people in the U.S.?� asks PolSci professor Alan Wolfe over at the Chronicle of Higher Education. Or, put in a more academic fashion, should the old Frankfurterian study “The Authoritarian Personality� be rehabilitated? Wolfe proceeds to answer in the affirmative. And how could one come to any other conclusion, considering the facts presented by Alan?

- Carl Ford Jr., a former head of intelligence within the U.S. State Department, once called John Bolton "a quintessential kiss-up, kick-down sort of guy."

- Sen. John Cornyn stated: “There are some activities so flagrantly un-American that, when responsible officials won't take the proper steps, the wide-awake citizen should take the law into his own hands."

- House Majority Leader Tom DeLay is in difficulty for his close ties to lobbyists like Jack Abramoff.

Clearly, only a pathological authoritarian could remain unconvinced of the rise of American Fascism after being presented with such an overwhelming body of empirical evidence!

PS.
More background here.
DS.

Amir Butler says, in reference to the hijab:

...This is complete nonsense. In reality, the wearing of the scarf is a non-negotiable religious mandate, enshrined in the Koran, and has nothing to do with politics.

In my post below I did not highlight that Winnifred Sullivan used the rise of an Muslim minority as a looming problem for religious freedom. Frankly, the post was overlong as it was, but it is a major issue-for-the-future. Islam is a religion that emphasizes orthopraxy, that is, proper practice of the laws and traditions of the religion. That being said, one of the most common things I have seen Muslims do when engaging with a non-Muslim audience is state flatly that "as a Muslim I must do x." The problem with this assertion is that there is a generally not an acknowledgement that, religion being what it is, it should have the qualifier "my interpretation." When a fundamentalist points to the Letters of St. Paul as justification for why women should not speak in church, many Christians have rough and ready responsive talking points.

The reality is the fact that many (most) Muslims believe that a given set of propositions are necessary conditions to the fulfillment of their religion has to be dealt with in whatever locality they are a substantial minority. That being said, too often I get the sense that questions relating to Muslims are simply assumed to be only answerable via Islamic referents. Not only am I skeptical that beyond-a-reasonable-doubt referents are going to be achieved in a liberal democratic regime (there is no D.C. mufti with supreme powers), we must ask if such referents should even be a primary consideration. Perhaps one should judge the wearing of the hijab, for instance, in the context of broader laws, social mores and goods, beyond the question of, "but is it required to be a Muslim?"

Barbara King reviews (via John Hawks) Steven Mithen's The Singing Neanderthal, and Richard Lewontin reviews The Evolution-Creation Struggle and Not by Genes Alone.

When I first read the first chapter of Winnifred Sullivan's The Impossibility of Religion Freedom I knew I had to check out the full book at some point (see Randall's extensive commentary). Well, I just did, it's only ~150 pages and the prose isn't excessively legalistic. The specific core of the book is the Richard Warner vs. City of Boca Raton case and its reference to the Florida version of the Religious Freedom Restoration Act, but the broader context is the relationship between the state and religion in a pluralistic society. Roughly, Sullivan makes the case that by the very act of specifically protecting "religious" freedom the state arbitrates exactly what is, and isn't, religious, and so violates the original intent of the state to remain neutral.

The details of the case in question are rather banal. Like many cities across the nation Boca Raton has specific regulations of how cementaries should be maintained, and over a period of several years a group of families created ad hoc shrines on their loved ones' grave sites. This was in violation of a local statute which stipulated that one should not place obstrusive objects on the site. The reality is that the city generally did not enforce the law, but a local survey suggested to the City Council that most individuals who frequented the cemetary tended to favor the provision. In short, at some point the ordinance was enforced (though Sullivan states that it doesn't seem to be enforced anymore), prompting about a dozen individuals to file suit under the Religious Freedom Restoration Act.

Legal details do not interest me, and I doubt I could regurgitate the specifics of the federal and state guidelines that are operative as to the enforcement of the aforementioned law. For me, the most compelling portion of Sullivan's narrative was when she illustrated exactly how ludicrous some of the exchanges were. Here is an exchange between the lawyer for the city and a plantiff:

Q: The marble chips that are there [the grave site], do they have any independent religious significance to your?
A: Independently, no. They serve a religious purpose for me. They are not, marble chips in and of themselves and are not holy in any way.

Q: Does the header have any independent religious significance?
A: No...

Q: And the edging stones have no independent religious significance?
A: Independently, no.

[my emphasis]

In pointing out the extent to which the city lawyer began decomposing the exact details of religious practice, I think Sullivan was expressing her sympathy with the plantiffs (she was an expert witness for them). Later the plantiffs brought in an Eastern Orthodox priest (of Anglo-Irish ethnic origin, he was a convert from Roman Catholicism) to ruminate on the specifics of Christian practice in a historical context. And so begins an exchange where the lawyers and the priest engage as to whether scripture and Christian tradition allows a cross to be placed vertically or horizontally, whether both, either, or neither, are acceptable in the various forms of Christianity. An Orthodox rabbi comes to testify as to Jewish traditions and law, and the judge, of Calvinist background, at one point begins to dispute aspects of Biblical interpretation (and suggests that if the Torah is used as a justification, that is acceptable, but the Talmud is too subject to historical influences).

As for the plantiffs, their own religious practice and beliefs came into question. It was clear that many of the Roman Catholics, of Cuban or Polish origin, held to a form of the faith that was not assimilated toward American Catholic norms. When called on to justify their funerary practices they had to appeal to family tradition and secondarily fallaciously extracted from the New Testament passages that didn't exist. Jewish plantiffs who tried to make the case for their own religious views had to explain why they didn't attend synagogue (too expensive) and elaborate on the details of difference between Jewish sects in the United States (the man was an English immigrant, so he had a hard time distinguishing Reform, Conservative and Orthodox). Additionally there was a great deal of time spent emphasizing the obvious importance of the Star of David to Judaism, but Sullivan points out that this symbol has become omnipresent as a outward representation of Jewish identity since 19th century Zionism. The City of Boca Raton was attempting to establish that the practices that the plantiffs held were religious were "personal," and they used as a standard the elite codified forms of the religion that they plantiffs nominally espoused to make that case.

At this point you can see where Sullivan's book is going, mixing a loosely worded and expansive law with a religiously plural society where clerical institutions have little arbitrative power is a recipe for confusion. Moving it a step further Sullivan offers that international agencies also need to be cautious in expanding the right to religious freedom in an unqualified manner.

I suspect most readers can connect the dots here. People may accept a religious precept which implies behavior in contradiction with the laws of the state. Additionally, religious precepts of different religions also often conflict and jockey for primacy in the public space. As an unbeliever it does irritate to some extent that by the very nature of an action being condoned by a religion, that action is often acceptable, or at least within the field of play, when in a non-religious context there would be no argument. For example, consider this practice:

The practice is known as oral suction [redacted]: after removing the foreskin of the penis [of an infant], the practitioner [redacted] sucks the blood from the wound to clean it.

Now, with the full context:

The practice is known as oral suction, or in Hebrew, metzitzah b'peh: after removing the foreskin of the penis, the practitioner, or mohel, sucks the blood from the wound to clean it.

There is an implicit operation, (act or belief) X (religion) = lower threshold of outrage and incredulity. In previous times, and different places, the operation is more like so, (act or belief) X (my religion) = lower threshold of outrage and incredulity. For some Westerners the operation has been transformed in the following fashion: (act or belief) X (!my culture) = lower threshold of outrage and incredulity. An an unbeliever I am not happy about this situation, but, as a realist I accept it as the way the world works. When the Mongol hordes were sweeping across Eurasia their leaders explicitly gave religious officials protection. Since the Mongols during this period did not adhere to a specific religious tradition they were simply currying the favor of the gods of the conquered nations, but, no doubt there was a utilitarian benefit in exempting the priests and turning them to their purposes when it came to mollifying and controlling a restless population.

Sullivan does a good job placing the peculiarity of American elite religion in its broad historical context. She contends that after the Reformation there was a process of deinstitutionalization, decentralization and individuation of religious belief and expression which has reached its apotheosis in the United States. Not only did the ensuing pluralism force the disestablishment of the church from the state in this nation, but the ever expanding range of beliefs and practices began to open wide exactly what were and weren't religious expressions. But I think she leaves the specifically American context a little thin on the ground, because in 1776 we were a very different nation than we are today.

In 1850 Archbishop of New York, John Hughes, stated:

...all Pagan nations, and all Protestant nations, even England with her proud Parliament...Everybody should know that we have for our mission to convert the world-including the inhabitants of the United States-the people of the cities, and the people of the country, the Officers of the Navy and the Marines, commander of the Army, and the legislatures, the Senate, the Cabinent, the President and all.

(source, American Catholic)

Though there have been many Protestant denominations, and later Jewish ones, who have risen and fallen in this nation, for much of American history there has been a special dynamic, or tension, with the Roman Catholic Church. It wasn't always so, the bishop John Carroll in the early 19th century presided over an American Church where foreign influences were minimal and local control was paramount. In the 1830s Congress even had a Roman Catholic chaplain, the very last one we've had. Carroll would speak of the Christian Catholic Church and was prominently ecumenical.

This changed in the 1840s and 1850s. There were many reasons. Part of it was the massive wave of Irish and German Catholic immigration, part of it was the turn against liberal nation-states on the part of the Vatican, and part of it was the emigre community of foreign priests and intellectuals who arrived in 1848 in the wake of liberal revolutions, failed and successful, who were skeptical of republics and liberal democracies.

In 1859 Thomas Whall, a pupil at the Elliott School in Boston, was beaten for refusing to read from the King James Bible (source Catholicism and American Freedom). A Roman Catholic, Whall was encouraged by a newly arrived arrived Jesuit who were agitating for the separation of his flock from Protestant society. Over time Roman Catholics were crucial in spearheading the move toward a more ecumenical religious program within the public schools (i.e., much of the nation no longer prayed Protestant prayers or read Protestant Bibles), even though eventually a great number of Catholic children were enrolled in the parochial school system. This assertion of independence and distinctiveness by the Roman Catholic Church elicited the nativism and Known Nothingism that was a hallmark of a strain of American thought deep into the 20th century.

Yet by the end of the 20th century there are surveys which suggest that young Catholics are skeptical about transubstantiation, charismatic Catholics are rejecting the institution of the Church while lay Catholics are appearing on television emphasizing that the sexual abuse scandal has had some effect on them, but they still value their "relationship to Jesus Christ" more than the Church. Of course, rejection of transubstantiation, the Church and acceptance of a direct relationship with Jesus Christ are hallmarks of Protestantism!

In Sullivan's book she offers that legal scholars are losing the forest from the trees, that religion as it is being lived amongst the populace is becoming a far more salient factor in our culture than the codified elite forms of religion that are familiar to intellectuals and easily integrated into rationalized frameworks. American Roman Catholics might not be what you would expect them to be based on the catechism of their church, but the late Pope John Paul II was also almost worshipped by devout Protestants in this country. Evangelical Protestants whose ancestors turned their backs on the imagery and pageantry of Roman Catholicism nevertheless flocked to Mel Gibson's movie.

On a basic level believers have I think always been far more similar to each other than the rational systems propounded by their clerics would have implied. With the decline in institutionalized religion this basal substrate is now coming to the fore, and a peculiar paradox of revived fundamentalism but operational ecumenicalism is making itself felt because conflicting beliefs become irrelevant when reflection is secondary to experience and emotion. But once reflection and centralized clerical codification become secondary or even marginal, the clear formalized relationship of a the polity to religions becomes impossible because legal forms and semantic precision can not map to the decentralized religious cults, sects and organizations that are proliferating throughout this nation. Couple that with the rise in a Post Modern relativist conception of culture, a tacit acceptance of "different ways," and the system needs to start facing its internal paradoxes.

Which brings me to my title, "A prayer for the Emperor." Church-state separation as we know it today is something of a peculiar thing. As Westerners we are well aware of the established churches of Europe, whether it be Anglicanism in England or Lutheranism in Scandinavia. In Germany some churches are privileged in that the state can collect voluntary tax from members (a coalition of Protestant churches and the Roman Catholic Church). But these models are presupposed on an ideal of an exclusivist and stand alone system of beliefs and practices. In the Muslim world a form of Islam, whether it be Sunni or Shia, plays the same role. Though Malaysia is a religiously pluralistic nation, the state takes a special interest in Islam and subsidizes the building of mosques.

But I think there are other models out there. The extent of religious pluralism in the United States is mind-boggling in comparison to much of Europe, where dominant religious institutions are embedded within the culture and often have associations with the state. Rather than modern Europe I think a better future model for the United States might be pagan Rome or Imperial China. In these states there really wasn't church-state separation, there was a public piety, and a mass of beliefs in syncretistic flux. Occassionally particular sects would cause political problems and the state would repress them, but in general beliefs were personal affairs so long as public order was maintained. Additionally, neither of these cultures was characterized by overwhelmingly dominant exclusive creeds with widespread institutional networks. The decentralized megachurches, the rise of para-church groups and the operationally expansive ecumenicalism that is becoming normative in the United States I think resembles this. People can not only "chuch shop," but cult formation is an ongoing process unmediated by political elites.

Because of their diversity, ultimately I suspect the religious orders and groups have to be either subordinate or oppositional to the state. This was the trend in ancient Rome or China. In contrast, Westerners have had a model where one a powerful exclusive religious institution strikes hard bargains with states as if they were equals (the Roman Catholic Church). Or, in nations like Norway, the national church has been absorbed by the state so the two are coterminus. The diffusion of religious power to innumerable bodies will inevitably result in the pulling back of the strong reverential stance that American politicians right now seem to take to all religions, so long as they aren't so deviant as to practice animal sacrifice. At least that's what I'd bet on.

Been awhile since I took a politics poll. I took this, and it said that I'm: "Social Liberal (75% permissive)" and "Economic Conservative (66% permissive)." No big surprise.

Update from scottm: Here are my scores. I'm: "social liberal (63% permissive)" and "Economic Conservative (81% permissive)". No big suprise here either.

I suspect most readers have perused Demonic Males at some point, and stumbled upon the concept of developmentally arrested orangutan males who mate with females by raping them (in contrast to the bigger males whose entreaties are welcomed). Here are two papers that readers might find of interest in relation to this topic....

Male orangutan subadulthood: a new twist on the relationship between chronic stress and developmental arrest:

...These results imply that the arrest of secondary sexual development in some male orangutans is not stress-induced, but instead perhaps an adaptation for stress avoidance during the adolescent or "subadult" period. These data, together with previously reported data on levels of gonadotropins, testicular steroids, and growth-related hormones, define endocrine profiles associated with alternative reproductive strategies for males with and males without secondary sexual features.

So why is this strategy hanging around? Well, Male bimaturism and reproductive success in Sumatran orang-utans:

Fecal samples were collected from a well-studied population in Indonesia, and eight human microsatellites were analyzed for 30 individuals that have been behaviorally monitored for up to 27 years. By carrying out paternity analysis on 11 offspring born over 15 years, we found that unflanged males fathered about half (6) of the offspring. Relatedness between successful unflanged males and resident dominant males was significantly lower than 0.5, and for some unflanged/flanged male pairs, relatedness values were negative, indicating that unflanged males are not offspring of the flanged males....

The data set is very small (though there aren't really that many orangutans to sample from out there, are there?). But I think it makes it clear that alternative reproductive strategies for complex organisms isn't unfathomable. It makes Henry's old ideas about father absence seem more plausible I think. Unfortunately the current ascendency of Evolutionary Psychology^TM allows the scientifically interested lay public to buy into the idea of phenotypic monomorphism, that there is one strategy to rule them all. And of course this results in bitch-fests between conservatives and liberals (or whatever typology you want to set up) aiming to lay claim to the mantle of ideology most in keeping with the Most Perfect Human Behavior.

Amusing biographical note from Sewall Wright and Evolutionary Biology:

...After Wright had clarified in the early 1920s the calculation of the degree of inbreeding in sexually breeding organisms, he calculated his own inbreeding coefficient. It was 6.3%, about one hundred times the average.

His parents were 1) first cousins and 2) Wright was descended from the Puritan stock of New England, so his genealogy was a tangle.

John reviews David Buller's book (what he's read so far).

What is a marmoset?:

Callitrichid primates typically give birth to twin offspring that are somatic chimeras of cells derived from two products of conception. Each individual is thus the phenotype of two sibling genotypes, one of which may be more closely related to the germ line of the individual's parents than to the individual's own germ line. Chimerism could therefore help to explain the evolution of alloparental care and social suppression of reproduction in callitrichids. Placental chimerism may also have important implications for understanding kin interactions within the womb: on one side of the coin, the intimate juxtaposition of genotypes provides unique opportunities for antagonistic interactions between embryos; on the other side, chimerism could facilitate cooperation between sibling genotypes.

Perhaps you already knew marmosets were chimeras, I certainly didn't. You can read the full paper (PDF)...David Haig works out some interesting genetical implications from the freaky premise. I'm not that disturbed on a moral level by marmoset chimerism, but I am a little surprised that a "complex" organism could habitually go through such a bizarre developmental mix & match process. Biology, the science of rules that hold, unless they don't.

Matt McIntosh pointed me to this correspondence to Nature from Scott Atran and Jessica Stern eludicating some of their ideas in relation to terrorist networks. They dovetail pretty well with Marc Sageman's argument. Here is an interesting point:

...We ask questions such as: "What if your family were to be killed in retaliation for your action?". Almost all answer that, although they have a duty to their families, their duty to God comes first. "And what if your action resulted in no one's death but your own?" The typical response is "God loves you the same". Such reasoning is not very sensitive to standard cost−benefit calculations or moral trade-offs.

These individuals are clearly not utility maximizers in a way we can relate to. In A Theory of Religion Rodney Stark and William Bainbridge develop a model of the growth and decline of religious "firms" borrowing rational choice terminology. Roughly, they argue that religions offer a bundle of supernatural goods and services (clerics are middlemen), and the success of a given denomination is determined by the nature of the goods and services that it provides to its customers. There are problems with Stark and Bainbridge's model, but, for the particular sort of believer that Atran and Sagemen have focused on it, it might be a decent approximation. I have already noted that Islamic fundamentalists of the transnational sort are often drawn from technical backgrounds, so they are well versed in structured propositional thinking. As Sagement documents the core of Al Qaeda tends to be sliced off from the intellectual elite of their respective peoples. Now, note this:

... A burgeoning literature in economics argues that bounded cognition can explain many observed empirical deviations from rationality. Consistent with this hypothesis, we show that individuals with greater cognitive ability behave more closely in accordance with economic decision theory. However, even the most cognitively skilled individuals display significant biases.

I have gone on record multiple times that I think theologies are usually quasi-propositional in character, that their "rationality" is to some extent achieved via scholarly consensus, not through the transparently obvious deductions inferred from the axioms. After all, it was long "obvious" that slavery was compatible with Christianity, and it has now been "obvious" that slavery is not compatible with Christianity (you can find appropriate chapter and verse for the former view, and crisp logical deductions for the latter). Nevertheless, over the full range of choices of quasi-propositional systems a literalist, but operationally antimonian, form of Islam is available and attractive to a particular subset of Muslims. This form of Salafist Islam is often highly reduced in character, paired down to a few core mandates and a host of supporting behavioral strictures. Extracted out from any social context (it has traditionally even assaulted the indigenous practices of Arabia itself!) it is a "product," a one-size-fits-all ideology that is easily exportable to the rest of the world because of its chilling simplicity. But this ideology is only a necessary condition for transnational Islamic radicalism, not a sufficient one. Social networks and communal rituals are the matrix in which the ideas bear poisoned fruit. Remember, smart people can implement dumb things better and more efficiently than stupid people.

This is not to say that I believe that Sageman and Atran are necessarily correct. Nevertheless, I think they offer the most textured and subtle of the models out there, and it seems to me that they do capture at least the principle component of the vector aimed at the heart of the West. We need to start somewhere as far as model building goes, we've taken succor from empty platitudes for far too long.

Addendum: Something Atran seems keen to emphasize that 80% of the post-9/11 Al Qaeda sympathetic activists seem to have an association with the Muslim Diaspora and their social networks are only 20% family. The latter number is pretty mind-blowing considering the cultural milieu that jihadists come from where extended family networks are paramount to the point of exclusionary toward non-kin ties. What one is seeing I suspect is the emergence of a new "cult" within Islam.

Related: Profile of Salafi jihadists.... Atran expands on his views in this piece.

As a follow-up to my post Postrel on the Anti-Science Left I'm pleased to turn the spotlight on the Moralistic Right. Media Girl reports on new legislation being advanced in Indiana:

According to a draft of the recommended change in state law, every woman in Indiana seeking to become a mother through assisted reproduction therapy such as in vitro fertilization, sperm donation, and egg donation, must first file for a "petition for parentage" in their local county probate court. Only women who are married will be considered for the "gestational certificate" that must be presented to any doctor who facilitates the pregnancy. Further, the "gestational certificate" will only be given to married couples that successfully complete the same screening process currently required by law of adoptive parents.

As it the draft of the new law reads now, an intended parent "who knowingly or willingly participates in an artificial reproduction procedure" without court approval, "commits unauthorized reproduction, a Class B misdemeanor." The criminal charges will be the same for physicians who commit "unauthorized practice of artificial reproduction."

The change in Indiana law to require marriage as a condition for motherhood and criminalizing "unauthorized reproduction" was introduced at a summer meeting of the Indiana General Assembly's Health Finance Commission on September 29 and a final version of the bill will come up for a vote at the next meeting at the end of this month.

Republican Senator Patricia Miller is both the Health Finance Commission Chair and the sponsor of the bill. She believes the new law will protect children in the state of Indiana and make parenting laws more explicit.

I'll leave it to you to discuss why the Republicans think that targeting unmarried women who can afford an expensive IVF procedure is permissable but controlling the fertility rights of other unmarried women is out of bounds.

This is almost like waving a red cape in front of a bull. A number of prinicples are being conflated here:

1.) The stability of relationships needed to raise a child is not only conferred by a marriage certificate;
2.) Single motherhood has negative consequences as we've seen with teen mothers, poor mothers, and mothers who don't provide a father figure for their children, but not being married while seeking IVF treatment does not necessarily equate to the negative social dynamics often associated with single motherhood;
3.) Opposition to lesbians becoming mothers when two lesbians committed enough to pay for, and go though an IVF procedure, are more likely to be good parents than many poorly dedicated married couples who accidently became parents.

Note that the definition of "mother" would seem to include women acting as surrogates.

The more of these reports that I read the more I think that the fundamentalist Right and Left should get together and leave the moderates of each party to coalesce into a counterbalance. See Turning of the Tide.

Over at Sepia Mutiny I got into a small argument with multiple people in regards to the Bali bombing, and its "root causes" and what not. I understand that politicians have to express vague platitudes, after all the public is so stupid that 1 out of 5 people think that the sun goes around the earth, but I'm not as patient with it on weblogs. Perhaps I should be, but here is the problem I have, people seem to transform Islamic fundamentalists into inscrutable forces of nature, capricious, irrational, maniacal and/or mentally ill. My main point was that one can have very strange and alien views and intents and still be rational. Rationally is the working out of inferences from starting assumptions, and if the axioms differ one would expect that the conclusions would vary. I hold that Al Qaeda and its ilk are rational in a fashion, that is, their behavior is not faulty reason or psychopathology, they have a coherent and clear world-view which they act upon (coherent and clear is a relative judgement, humans are fuzzy about values and the meaning-of-the-world). That doesn't mean that I agree with their world-view, their reasoning can be defended from where I stand (looking at the broad sweep of Islamic history I think it has clear precedents), but their axioms need not be conceded or apologized for. Recasting them as vague and almost elemental beings who we don't have reason to understand really pisses me off, because this sort of attitude gives everyone a free reign to propose multitudinous solutions. Without any theoretical framework to conceptualize and model the problem our only recourse in guides to picking a solution are particular biases and norms which might not steer us to the optimal response. In other words, you need to understand local weather dynamics before you decide to build a bridge across a gorge. Instead, people strike me as looking for hexes and amulets to defend themselves against the demons that rage in the night. When you point out to them that men, not demons, are the source of their evil and that their hocus-pocus recitations of communally agreed upon mantras doesn't do jack-shit, people get pissed....

Update: Please address what I said, not what you think I said, or what you think I believe. My contention is rather narrow, a rational way of thinking has its place, even when it comes to world-historically significant clashes of civilizations. Passion and ferocity also has its place, but from what I can see there is plenty of passion and ferocity in evidence. David Hume said that "Reason is, and ought only to be the slave of the passions." I agree, the norms and premises we accept are to some extent outside of reason, they are common points of reference between fellow travellers. The slavery of reason has no moral cost, it does not suffer when we use it toward our ends. Granted, it is a difficult servant, and only a few can truly be bothered to master it, but it seems that far too many of those who could snap the whip to reason have abandoned their role as hard field masters for the more congenial company of the house slave that is passion for the sake of passion. And yet in the end it is the laborers in the field who provide the sustenance for the big house.

Update II: I wasn't going to make this analogy, but think of the Bene Gesserit. They use passions as tools, but don't delude themselves into thinking that their tools are anything but that.

I noticed that the Annual Review of Genomics and Human Genetics had a paper titled Human Taste Genetics up, so I put it in the gnxp files as "taste." I've posted on taste before (see here, here, here and here), so I thought readers might find it interesting. One point to note is that the author suggests that his own research points to the possibility that non-tasters for PTC might not actually be a typical loss-of-function mutation (ie; the old model was that non-tasters were recessive homozygous), but rather they could be cued toward another type of bitterness that has not been properly characterized. Note how other taste qualia, like sweetness, are often described as having a narrow unimodal distribution. This might be indicative of strong directional selection purifying most of the genetic diversity so that most humans are fixed for a particular trait. As the paper notes most of the variation seems currently related to the bitter tastes (though Africans seem to have more than the typical amount of taste variation, one case where they are the most diverse peoples in the world).

Folk science tells us that the Cambrian Explosion was the source of all the body plans that we see around us, an evolutionary miracle where morphological diversity emerged fully formed from the brain of Gaia (i.e.; bilateral vs. radial symmetry). Some Creationists use this to argue that God created all these creatures specially, and the famous Hox developmental gene family were the tools which aided God in his design. Of course, geological time isn't the same as our own intuitive gestalt perceptions of what an instantaneous "explosion" is like. A few years ago the paleontologist Andrew Parker, in his In the Blink of an Eye, argued that the development of vision was the crucial prod that resulted in the proliferation of multicellular (hard-bodied) life. My post about the Pax gene family suggests that we should be cautious about such an explanation, since the smoking gun of a shared derived character doesn't seem to fit well in the case of vision (synapomorphies vs. symplesiomorphies).

If any of these issues strike your fancy, I will point you to two papers, The dawn of bilaterian animals: the case of acoelomorph flatworms and The Hox gene complement of acoel flatworms, a basal bilaterian clade. The short of it is that the Hox gene family itself, that most wonderous of toolkits, has likely been tinkered with by evolution. The action in these papers centers on the animal node of the tree of life, it seems that the 8-10 Hox gene complement characteristic of vertebrates and most of those we colloquially know as invertebrates developed in stages, likely via gene duplication, from the common ancestor which the Bilateria share with the less complex taxa. In particular, the papers above suggest that one group of bilateria, a branch of the Platyhelminthes termed the Acoela, might be misclassified, and that their true cladistic position is basal, the outgroup, to the two great families of deuterostomes and protostomes. This group exhibits only some of the Hox genes characteristic of the bilateria. The normal explanation, the most parsimonious one, would be that these genes were lost over time (this is known to have occurred among the nematodes), assuming the old cladistic position. But the authors of the papers above point out that multiple loci now point to a misclassification and a basal location in the phylogenetic tree vis-a-vi other Bilateria. In the second paper they assay two distantly related species of Acoela and offer that the loss of genes hypothesis is implausible, and the minimal set of Hox is likely an ancestral characteristic. Additionally, they point out that that non-Bilaterian animals tend to exhibit this minimal set as well. They conclude that the Hox genes went through duplications during the evolution of bilaterians. There are many assumptions that the authors make, and certainly this is not a well established field (i.e.; evo-devo), so findings and analyses are extremely provisional, but the message is that the revolution that occurred in the minds of evolutionary biologists when the conservation of Hox genes was discovered should not blinker us to the reality that change is still a constant when it comes to natural history, and even tools get tinkered with.

NOISE AND DELAYS EXPLAIN WHY SOME GENES OSCILLATE IN ACTIVITY

“unscripted biochemical variations, or noise, combined with time delays in certain biochemical reactions may lead to oscillations in gene regulation that couldn’t otherwise be predicted. Such noise is routinely described by cell biologists who record large phenotypic differences between supposedly identical cells in a single flask of growth medium.�
…
“The fine-grain fluctuations we see in the genetic regulation within single cells may lead to new insights about variability at the level of the whole organism�


Noise is under appreciated. Some speculation on noise…

Noise prevents sharp “edge� effects. Imagine a thermostat with no “noise�. Too cold then turn on, too hot then turn off, the heater would be continually turning on and off. Slop in a steering wheel is another example. If the wheel is too responsive then the driver over corrects.

“Noise� in the genome: Mutations generate new gene alleles. If the new allele significantly improves fitness then it rapidly increases in frequency. If the new allele significantly decreases fitness, then it may disappear. But many mutations won’t have much of an effect either way. Such gene alleles act as genetic “noise�. Such genetic noise produces statistical “outliers� that are extreme phenotypes. (E.g., very high IQ.)

Gene allele “outliers� provide feedback. If the environment changes so that the “outlier� significantly improves fitness then that gene allele frequency increases and the population rapidly adapts. Negative “outliers� would “push� the population away from the “bad� allele. Thus noise makes the genome more robust and stable.

Molecular noise provides the random generator needed to for our body’s immune system to build broad coverage against potential invaders and generate new antibodies to specific molecular targets against invaders that make it past the first immune barrier.

Noise can provide the “mutations� in a Darwinian mechanism such as might occur in thinking and skill learning. (Similar to “heat� in simulated annealing.)

Noise keeps certain neuronal systems healthy. Too little noise can lead to heart attacks or seizures.

Update from Razib: Look in the gnxp files for "noise," that is the PDF of the paper that the article is based on.

Just a small real-time reflection: Watching reactions to the Miers pick among the GOP base over at www.freerepublic.com, it strikes me as if it's not going down too well.

Another small reflection: Is pissing off the base really the right move for Bush right now? ("Tipping point" is more than the title of a Gladwell book...)

Ronald Bailey, in an article over at reason, points out one unintentional consequence of Bush's funding restrictions:

The National Institutes of Health spent $24.3 million dollars on human embryonic stem-cell research last year. Critics of President Bush's policy of limiting federal funding to only those stem-cell lines derived before August 2001 worry that this amount—relative to NIH's annual $30 billion budget—is not enough. Persuaded of the importance of this research, the U.S. House of Representatives voted in May to lift President Bush's funding restrictions. Senate Majority Leader Bill Frist announced this summer that he supported that legislation. The Senate is poised to vote on the issue later this fall.

But do stem-cell researchers really need the feds? Already there is nearly $4 billion in private and state monies committed to stem-cell research over the next decade, with another three-quarters of a billion dollars under active consideration.

I find it amazing and heartening that the non-Federal sector has stepped up and committed 16.4 times that what the Feds have (assuming $243 million over a decade from NIH) and makes me wonder what other areas might be better served by a switch to non-NIH funds for some areas.

Look, I'm no utopian Libertarian, I know there are areas of research (and specific parts of some general areas) which won't be funded privately because they don't show any promise of profit anytime soon. And I know that a lot of this funding comes from other government bodies ; but I think there are areas that now suckle off of Uncle Sam's breast who need to be kicked out of the Treasury nest and find their own funding. This would free up a lot of cash for more "pure" research projects, and advance our nation's general knowledge of science.

Just my thoughts.

Virginia Postrel has an informative piece in the current issue of Forbes on Canada's Leftist attack on genetic science.

U.S. scientists and their supporters tend to assume biomedical research is threatened by know-nothings on religious crusades. But as the Canadian law illustrates, the long-term threat to genetic research comes less from the religious right than from the secular left. Canada's law forbids all sorts of genetic manipulations, many of them currently theoretical. It's a crime, for instance, to alter inheritable genes.

And the law has provisions the fabled religious right never even talks about. It's a crime to pay a surrogate mother or to make or accept payment for arranging a surrogate. It's a crime to pay egg or sperm donors anything more than "receipted expenses," like taxi fares. Since eggs are used not just in fertility treatments but in research, this prohibition stifles both. . . .

You can't say the same for the antibiotech left. In liberal Canada, in fact, the law defines cloning expansively. Future procedures that might avoid religious objections would still be illegal. The goal is to stop certain research altogether.

What Postrel may not be aware of is that Canada has a law which mandates the creation of a registry to record the birth of children conceived with IVF. Bill C-13 paragraph 17 reads:

The Agency shall maintain a personal health information registry containing health reporting information about donors of human reproductive material and in vitro embryos, persons who undergo assisted reproduction procedures and persons conceived by means of those procedures.

It's odd that those who fight for reproductive rights and the privacy inherent in the very question of whether to have children or not were completely silent on the creation of an Agency to record the very reproductive choices that people are making and the notation of the children born of IVF. We're all aware that government intrusion most always starts with the collection of information, and I see no reason for government to intrude into the personal issue of reproduction, and I fear where governmental mission expansion will lead with regards to reproductive rights.

Imagine the outcry if a government Agency was started with the stated purpose of recording the birth of children born with red hair, or of Ethipoian heritage.

No explanation was offered for why children born of IVF need to be noted in a database. What sets these children apart from others, even from those who are adopted?

Postrel is right, it's the Left that poses the greater danger here.

Related: The Seeds of Star Trek in German Politics, The Conflict Within - The Left's Version of Creationism and Know thy Enemy - "Newton's Rape Manual"

Thanks to Instapundit for the pointer.

Hsp90 Potentiates the Rapid Evolution of New Traits: Drug Resistance in Diverse Fungi:

Hsp90 is a molecular chaperone for many signal transducers and may influence evolution by releasing previously silent genetic variation in response to environmental change. In fungi separated by ~800 million years of evolution, Hsp90 potentiated the evolution of drug resistance in a different way, by enabling new mutations to have immediate phenotypic consequences. Resistance was abrogated by Hsp90 inhibitors and by febrile temperatures, suggesting new therapeutic strategies and a clinical benefit of fever. During selection in a human host, drug resistance that was initially Hsp90-dependent evolved toward independence. Thus, Hsp90 can act in diverse ways to couple environmental contingency to the emergence and fixation of new traits.

This article, India is China's economic equal, Bah!, has a nice point-by-point numerical comparison in a table. Sample: under 5 malnutrition, India 45.8% vs. China 12.1%. Sometimes journalistic innumeracy has its consequences. A philanthroper like George Soros should fund a new paper where the journalists were all recruited from mathematics, statistics and econometrics. It might make dismal copy, but at least there would less obfuscation of the world as it really is via verbal dodges (i.e.; "many," "growing trend").

Via Sepia Mutiny.

I suspect many readers will find a lot of food for thought in Structure and Dynamics: eJournal of Anthropological and Related Sciences. Thanks to board member Cosma Shalizi for the pointer. Hopefully this will further the shift from description to modelling. It shouldn't be a surprise, dynamical systems is an up and coming paradigm in cognitive science, it's just crawling up the ladder of human complexity now (or is it?).

I have mentioned the Pax6 gene before in relation to myopia, but recently I stumbled onto this review paper/model proposal titled Pax genes in eye development and evolution (you can find the full PDF in the forum files as "kozmikpax"). Many of you are probably aware of the shocking level of conservation of hox genes across animal taxa, but this sort of evolutionary developmental similarity on the genetic level is probably rather common (to the surprise of biologists when this was first discovered a few years back). Though creationists like to point to the eye as an example of an organ which bears all the hallmarks of design, it is an interesting observation that the structure of this particular sensory apparatus varies a great deal from species to species (compound insect eyes vs. the vertebrate eye vs. the cephalopod eye). Some groups of animals, like cave fish, also tend to lose their visual capacity when selection for the character is relaxed.

The Pax family of genes, of which Pax6 is a prominent member, produce transcriptional factors¹ which are implicated in a host of regulatory functions as relates to the development of eyes across many animal taxa. The author points out that:

• The Pax family is found in animals which have no visual apparatus or neural network.
• The most recent common ancestor of all the Pax genes seems to predate the geological age when vision became a ubiquitous feature of animals.
• In mammals particular Pax genes that are involved in eye development in invertebrates are to be found in the glial tissue. This is, different family members have different roles across taxa.
  
• Though Pax genes seem a necessary condition for normal eye development, they are not a sufficient condition (there are other genes which are involved in eye development).

The phylogenetic and comparative points of evidence suggests to the author that the Pax family originated prior to the evolution of vision, and that it was coopted multiple times over the course of natural history. The implication here is that convergent evolution not only produced "eyes" in a variety of taxa, but the same gene family was recruited for this developmental pathway each time! It is important to note though that the review points out that in vertebrates more functional diversity is squeezed out of these genes via alternative splicing while in invertebrates duplication is the norm.²

Ultimately the author suggests that the reason that Pax has been recruited is rather prosaic. He offers that the minimal characteristics of a visual sensory apparatus include a photoreceptor an dark pigment, no matter what variation is the norm on other structural features. The Pax family tends to have two binding regions³ which can be regulated in a coupled fashion, so the gene can map onto the appropriate functional pathways. The reason that Pax, and not some other gene with two binding regions, is preferentially recruited for its role in the development of the eye is unclear, though one can spin stories of pre-adaptations unconstrained by pleiotropic effects with negative fitness consequence pretty easily.

A more parsimonious explanation is that the Pax family has always played a role in eye development, and in cases where it isn't implicated in eye development it is a loss of function. Though the points that argue against this are highlighted in the paper, I can't quite give up on this avenue because of its simplicity.

There are many philosophical issues wrapped up in the resolution of questions rooted in the "problems" that evolutionarily developmentally salient loci like the Pax family pose. Interesting times....

Addendum: If eyes were each special creations, god seems an old dog that can't learn new tricks.

1 - Transcription is the mapping of DNA to RNA, which is eventually translated into proteins. Transcriptional factors turn up or down the cranks on genes which are normally spinning off RNA into the aether.

2 - Gene duplication is pretty straightforward (relatively), but splicing is weirder.

3 - Binding regions are parts of the DNA helix where transcriptional factors lodge themselves and either turn up or turn down transcription. Turning off is pretty common sense, since a foreign object just shows up on DNA's door. But sometimes the factor has all sorts of weird extensions which might aid in the initiation of transcription.