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May 27, 2005
Why humans beat elves
In Mutants Armand Leroi reviewed the antagonistic pleiotropy theory of aging. Of course, anyone who reads fantasy books would understand this intuitively, no matter how primo Elf traits are (long life, superhuman vision or agility, magical powers, etc.) short-lived humans are always more numerous and dominant because of their fast reproductive cycles.
Anyone engaging in a Fred Reed impersonation, that is, talking about shit they know nothing about shamelessly and without any humility in light of their ignorance, will now be deleted at my discretion.
May 26, 2005
More selection on mtDNA
Of course Parkinson's disease effects the old so selection pressure probably isn't that great (though older family members can have fitness effects down the generations).
Short takes on 3 books
Over the past two weeks I've been reading three books on my spare time, some short takes now that I've finished all three.
Desperately Searching for Eurabia
Eurabia represents a geo-political reality envisaged in 1973 through a system of informal alliances between, on the one hand, the nine countries of the European Community (EC) which, enlarged, became the European Union (EU) in 1992 and on the other hand, the Mediterranean Arab countries. The alliances and agreements were elaborated at the top political level of each EC country with the representative of the European Commission, and their Arab homologues with the Arab League's delegate. This system was synchronised under the roof of an association called the Euro-Arab Dialogue (EAD) created in July 1974 in Paris. A working body composed of committees and always presided jointly by a European and an Arab delegate planned the agendas, and organized and monitored the application of the decisions.
There are many problems with Bat Ye'or's thesis. Most immediately, quite apart from assuming unrealistic motivations for everything from European foreign policy to immigrant demographics, she severely overestimates the functionality of the international organizations that she cites.
For instance, searching on Google for the keywords "Euro-Arab Dialogue" returns a bit over four thousand, up from under a thousand the last time I checked, back in 2002. There's even a two references to the Euro-Arab Dialogue in the top 10 hits returned by Google which aren't Ye'or's endlessly copied articles. This compares to 33.5 million hits for "European Union," 439 thousand for "Commonwealth of Independent States," a bit over three million for "ASEAN," 3.7 million for NAFTA, and almost 1.4 million hits for "Mercosur" or "Mercosul." I'd have expected that such an important group as the Euro-Arab Dialogue--the central body behind Eurabia, after all--would have a bit of a higher presence outside of Ye'or's literature than it does. Surely more people would have noticed by now?
Then again, reading the various non-Ye'or descriptions of what the Euro-Arab Dialogue is supposed to do and what it has actually done, I begin to suspect that accepting Ye'or's thesis about the Euro-Arab Dialogue is something like believing that the Canada-Taiwan Parliamentary Friendship Group is actually a mechanism intended to ensure Canadian military participation in Taiwan's upcoming war of independence against China. As for the Arab League, I fear that it has lost whatever tenuous coherence it once had once Egypt decided to break with the League and sign the Camp David Accords. It isn't as if the Arab League has ever been as capable a body as the European Union, mind, as the failure to unify the Arab states in any meaningful way demonstrates.
This thesis also misreads the balance of power between the European Union on the one hand and the Arab states on the other. Yes, (some) Arab states have oil. The European Union is the $US 12 trillion First World economy that is a preferred destination for immigrants from the Arab world and a necessary source of much of the civilian and military technology used in the Arab world. The European Union is a global economic power with significant cultural and political influence worldwide, hence, numerous partners apart from the Arab world: Russia, South America, China, India. If any side is the hegemon in this relationship, it's the European Union.
While other policies--those relating to the Middle East peace process, those relating to the Persian Gulf--play a role, the European Union's relationship with the Arab world is dominated by the Euro-Mediterranean Partnership. The Euro-Mediterranean Partnership's stated goals are threefold: establishing "a common area of peace and stability through the reinforcement of political and security dialogue"; building "a zone of shared prosperity through an economic and financial partnership and the gradual establishment of a free-trade area" by 2010; and, encouraging a "rapprochement between peoples through a social, cultural and human partnership aimed at encouraging understanding between cultures and exchanges between civil societies." Unfortunately, the Partnership's lofty hopes, as Hüseyin Isiksal notes in his paper ("Security, Globalisation, and Problems within the Euro-Mediterranean Partnership in the post Cold War Era") (PDF format) may go unfulfilled. The implementation of the Partnership has gone slowly, with declining foreign investment in the Arab world and a rather fraught relationship generally between Europe and the Muslim world generally boding ill. The goal of establishing a free-trade zone by 2010 seems to be as realizable as the European Union's Lisbon strategy to become the world's most competitive economy by 2010.
Central Europe has easily beaten the Middle East and North Africa into the ranks of the European Union. More, it's quite possible that the former Soviet Union will follow the central European trajectory, with countries like Ukraine, Moldova, and Georgia hoping to become member-states. The Eurabia thesis would seem to predict that the Middle East and North Africa would do rather better than either of these two regions. Even Turkey, a country with a long history of participation in European institutions, might well not get in. Although it is
Such potential candidates as Morocco and Tunisia can expect to be eternally outside of the Union's gates, to say nothing of such implausible candidates as Algeria, Libya, Syria, and Egypt. Quite apart from the fact of not being geographically European (and, it must be added in this era of civilizational clashes, culturally European). none of these states as yet meets any of the political, economic, or social preconditions for European Union membership. Arguably, radical republican dictatorships, conservative republican dictatorships, and conservative traditional monarchies are incapable of participating in structures like those of the European Union, lacking the flexibility and the transparency and the functionality of democratic regimes. Free-trade regimes are a different thing--China has notably achieved economic success in the past-quarter century despite its dictatorship--but as the various Arab Human Development Reports suggest, most of the non-oil economies of the Arab world are at best able to keep pace with population growth.
So. The European Union, contrary to the arguments of the Eurabia hypothesis, isn't rushing into an ill-thought subordination under Arab rule. If anything, it's decidedly reluctant to involve itself with the Arab world at all, favouring trade with China and immigration restrictions against the Third World and mandatory government assimilation programs. The most readily testable plank of the Eurabia argument is unsound.
I wrote back in January that one major failing of the Eurabia argument is its sheer danger. If it's impossible for Europeans to agree with Arabs (or Muslims; there's always some semantic slippage) on certain principles of foreign policy, or for Europeans and Arabs to enjoy mutually beneficial trade or to enter into grand political projects or to engage in a "dialogue of civilizations" (whatever that is), or for Arabs (and other Muslims) to be loyal citizens or honest partners, then the implications are both vast and obvious. Genocide and ethnic cleansing are two methods which have been used to control inconvenient or threatening populations within a state's frontiers; aggressive war and colonization are two methods which have been used to control inconvenient or threatening populations outside of a state's frontiers. If ever the peoples of the European Union bought the Eurabia thesis--if any nation-state did--we could expect bad times ahead.
Granted that Eurabia is a concept that lends itself easily to racism, people who accept it are not automatically racist. Myself, I admit that before I completed my post last year on the demographics of French Muslims, demonstrating that, in fact, they are assimilating, I thought it at least possible that Europe might become substantially Muslim and that some parts of Europe could become Muslim-majority. Fortunately, I think that there's a litmus test that can be applied.
In the mid-2010s, a series of peaceful democratic revolutions and negotiated transitions establishes fairly secure and generally secular regimes throughout the Middle East and North Africa. Things are shaky, but no more shaky than they were in Argentina or Brazil in the mid-1980s, or in Poland and South Africa in the first half of the 1990s. The new governments respect human rights reasonably well, religious pluralism is put on a strong footing, and the rights of women are acknowledged as realities. In an environment where the fears of a threat to Europe from its southern neighbours are no longer remotely plausible in the presence of peaceful regimes, would it be a good idea for the European Union to relaunch the Euro-Mediterranean Partnership or not?
The idea behind the Euro-Mediterranean Partnership makes sense. The ideal of balanced and reciprocal relations between the two sides of the Mediterranean is a good one. Fernand Braudel was right: There really is a Mediterranean community, having transcended barriers of nationality and language and religion to form a single whole for at least a millennium. This community isn't going to do well when everyone's girding themselves for Huntington's clashes of civilizations. When people aren't afraid that their neighbours are going to descend on them and murder them, why stop this community from forming? Rules-based systems tend to produce better results than anarchical systems, after all.
Fearing and hating the idea of a takeover of Europe by Muslims is one thing. Fearing and hating all Muslims indiscriminately is quite another. Sometimes, reading Bat Ye'or and the other die-hard proponents of the Eurabia thesis say about the 21st century, I worry that they think that Europeans and Arabs should have anything to do with each other at all. Bigotry is never a good foundation for scholarship, or for policy.
May 25, 2005
Will leave this new one up for about a day. Say yay or nay in the comments.
Update: If you think you have a cool logo design for gnxp's header, email it to me at contactgnxp - at - gmail.com. Small images with transparent backgrounds preferred (so a GIF). Will take submissions for a few weeks.
Update II: Changed it back. Send me new logos if you want though. Might test them out.
A matter of perspective
A week ago a mildly positive profile of the doyen of the Intelligent Design movement, Phillip Johnson, appeared in The Washington Post. I was going to comment on the relationship between Johnson's positive comments about Critical Legal Studies and the Anabaptist takeover of Munster in 1534 until other time sensitive tasks came to pressing attention, nevertheless I want to take a moment and point something out that I noticed. Note:
Here is Provine's research project as listed on his website:
The point is that anyone who is in-the-know would recognize William Provine as a prominent historian and philosopher of biology, not an evolutionary biologist, though he is based out of the ecology and evolution department at Cornell. Provine wrote a great intellectual biography of Sewall Wright, where he argues that the University of Chicago biologist was the most influential evolutionist of the 20thcentury.1 I think Provine's status as a student of "meta-biology" (since he focuses on history and philosophy of biology) explains his excitement in debating Johnson, for rhetoric and disputation scaffolded by logic would likely come naturally to him as a tool of the trade. Not so for real scientists who are busy focusing on the minutiae of lab work or the esoterica of mathematical models.
As I have noted before the sophisticates who man the turrets in the Intelligent Design movement are skewed toward philosophers and other like-minded disciplines (though there are a smattering of natural scientists like Michael Behe). That is why I oppose the argument that bringing Intelligent Design into the classroom will aid in the understanding of evolution in any way, it is in essense a philosophical challenge to methodological naturalism, not an alternative research program. Until proponents of Intelligent Design start up an alternative nuts & bolts laboratory based research program (see what Michael Behe focuses on in his day job as a biochemist, his technical papers have little to do with Intelligent Design, those are all to be found in debate-focused books and philosophical and essay oriented journals) meta-biologists like Michael Ruse and William Provine are their true adversaries, not the scientists. Seeing as how most high school students aren't even familiar with the basic foundations of Western philosophy I find the intellectual arguments for exploring the frontiers and margins of modern philosophy of science uncompelling (the political arguments are a different matter, since they can start from so many different axioms).
1 - This is a defensible assertion, seeing as how Wright lived for 99 years and was the primary theoretical influence on thinkers based in America like Dobzhansky and Mayr (and you can connect many evolutionary biologists in the United States to these two individuals). Nevertheless, I think one can not underestimate the prodding influence that R.A. Fisher had on Wright's exploration of the mathematical geography of evolutionary genetics (see both Provine's book and R.A. Fisher, the Life of a Scientist). Without R. A. Fisher there might never have been a Sewall Wright as we remember him today.
Dream takes root
How did they do it?
Once a significant number of blight-free trees are produced, new crosses could potentially restore the full genetic diversity of the American Chestnut tree, with blight-resistance. Maybe we'll get our American Chestnut forests back. I can't wait!
(Cross-posted at Rishon Rishon.)
May 24, 2005
Math & Science, in the public's interest
Well, maybe not so noble......
If you search through the GNXP archives, you'll see periodic references to how media, in general, negatively portray math/science (e.g., it is often the ``evil villains" who are the geniuses). A colleague at the Clinic I work brought me a videotape of a show called Numb3rs to watch (at work). 1 After watching the part of the season he brought me, I have to say I am almost impressed.2 Instead of the evil-mad-scientist caricature, they have a very positive slant on math/science, with a genius-can-help-the-commoner caricature (perhaps due to the show's consulting firm). Of course, they do portray the genius-in-residence as somewhat aloof and out of touch, but when you decide to devote a whole show to regression-to-the-mean, what can you expect? Still, the fella gets the last laugh, as his mentee-come-girlfriend is kinda cute (see below)
2. The (forensic) psychology is hokey. Truthfully, I've yet to see a 1/2 accurate portrayal of a (non-psychoanalytic) psychologist.
Dienekes recently drew attention to an important forthcoming article on altruistic punishment. The article has now appeared: James H. Fowler: Altruistic punishment and the origin of cooperation, Proc. National Academy of Sciences, May 10 2005, vol. 102, 7027-49. It is available as a free pdf download here.
So what is altruistic punishment and why is it important?
One of the central problems of human evolution is to explain the widespread existence of cooperation. Such cooperation often produces a benefit for social groups as a whole, but at a cost to the cooperating individuals. So there is an advantage for ‘free-riders’ who take the benefits but avoid the costs. Why then does cooperation not break down?
The problem can obviously be solved if free-riders are punished. But those who do the punishing incur a cost in doing so (e.g. the risk of retaliation), greater than their individual gain, hence the term ‘altruistic punishment’. So why should anyone punish?
Again there is an obvious solution if failure to punish is itself punished. We can avoid an infinite regress of special rules about punishment by adopting a general social rule to the effect ‘punish all breaches of social rules’. Since this is itself a social rule, failure to punish is also a breach of a social rule, which must therefore be punished, and so on.
Such a rule is an evolutionarily stable strategy provided a large enough proportion of the population are already following it. But it is difficult to see how the rule could become established in the first place. Several theorists have resorted to an explanation by group selection: in small groups a large proportion of ‘punishers’ may be established by chance, and these groups then spread at the expense of other groups.
Group selection should be regarded as an explanatory last resort. The importance of Fowler’s paper is that it provides an alternative explanation of altruistic punishment based on individual selection. If the only strategies allowed are ‘cooperate’, ‘free ride’, and ‘cooperate and punish’, then ‘cooperate and punish’ will be more costly than the alternatives when it is rare, and it cannot spread by individual selection. The crucial feature of Fowler’s model is that it allows another strategy: individuals can opt out of group activities when the benefit of cooperation is lower than that of individual activity. If there are too many free-riders, more individuals will opt out and ‘do their own thing’. But when most of the population have opted out, the strategy of ‘cooperate and punish’ may have an advantage over ‘opt out’, which allows it to spread even when it is rare. The strategy ‘cooperate’ (but not punish) will spread more quickly at first, but once ‘cooperate and punish’ has passed a certain critical frequency (which depends on the parameters) it gains over ‘cooperate’ until it becomes the prevalent strategy. So ‘cooperate and punish’ cannot spread when it is rare in a population consisting only of ‘cooperators’ and ‘free-riders’, but the existence of the ‘opt-out’ strategy gives it an entry point.
Fowler considers a number of possible objections to his model. I am not sure that the model is very plausible, but it is no worse in this respect than the group-selectionist alternatives. It does at least mean that the groupies can no longer claim there is no alternative.
Personally I think that both approaches are misconceived. The basic flaw is encapsulated in the first sentence of Fowler’s paper: ‘Human beings frequently cooperate with genetically unrelated strangers whom they will never meet again, even when such cooperation is individually costly’.
Well, no, they don’t. Even in modern, well-regulated societies such cooperation is unusual. (When did you last do it?) In hunter-gather societies, which prevailed for most of human evolutionary history, it is practically unknown. But I will expand on my objections in another post.
May 23, 2005
The Middle Model
Genomics refutes an exclusively African origin of humans. This is a long and complex paper, but intelligible with close reading. I have cut & pasted the introduction and discussion below. But I want to highlight one point:
The point about assimilation of the MC1R alleles from archaic populations matches what a GNXP commentor postulated earlier today. Please note that model presented above matches (down to semantics) what was outlined in Dragon Bone Hill, though with far greater clarity and precision.
Since the discovery of apparent signals of strong late Pleistocene population expansions (Rogers and Harpending, 1992 and Harpending et al., 1993) in human mitochondrial DNA (mtDNA), a number of studies have sought similar signs in other genetic polymorphisms. Among the data so analyzed have been nuclear sequences, short tandem repeat polymorphisms (STRs), and single nucleotide polymorphisms (SNPs). While mtDNA shows signals of recent expansions in almost every human population, it has by now become clear that the nuclear data do not present an unambiguous picture regarding population expansion associated with the spread of anatomically modern humans. For example, various analyses of STR data using different statistics have given contradictory signals of expansions, their timing, and the sub-populations involved (Di Rienzo et al., 1998, Reich and Goldstein, 1998, Kimmel et al., 1998 and Zhivotovsky et al., 2000). The first detailed evidence from the nuclear genome also showed no evidence at all of expansion (Harris and Hey, 1999).
To explain low interpopulation diversity in humans, it has been suggested that humans passed through a bottleneck (Haigh and Maynard Smith, 1972). It has also been proposed that there was a bottleneck associated with the emergence of modern humans in Africa and their spread throughout the world (Jones and Rouhani, 1986). For example, SNP haplotype block data show a signature of bottlenecks at vastly differing times in the prehistory of African and non-African populations (Reich et al., 2001 and Gabriel et al., 2002), even if their cause as yet remains unclear. These bottlenecks would need to have been of extraordinary severity and/or duration to explain some of the data, e.g., for Europeans, Reich et al. (2001) suggested a pre-expansion bottleneck size of 50 individuals for 20 generations (or any size and duration of the same ratio), while Marth et al. (2003) obtained their best fit with size-duration ratios between 1000 to 2500 individuals for, respectively, 240 to 550 generations. Yet, single locus studies (e.g., Harding et al., 1997, Harding et al., 2000, Zhao et al., 2000, Yu et al., 2001 and Yu et al., 2002) often find at most mild bottlenecks, or none, in non-Africans, resulting in an overall picture that is puzzling. A recent study by Marth et al. (2003) used 500,000 SNPs to conclude that the dominant population history of humans was a Pleistocene population collapse followed by a mild post-Pleistocene recovery. The importance of these varied signals of bottlenecks and expansions is the subject of this paper.
The significance of genetic signatures of late Pleistocene population expansions is that they directly address the contrasting theories of modern human origins that have been the subject of much debate since the 1980s. The recent African origin model (Cann et al., 1987 and Stringer, 1992) proposes that anatomically modern humans arose in Africa around 130,000 years ago as a new species, which subsequently spread across the world, replacing all non-African archaic humans. In contrast, the multiregional evolution model proposes that modern humans emerged across the world from regional archaic human populations that were always linked by gene flow (Wolpoff et al., 1984).
Genetic evidence to date has been interpreted as giving far greater support to the recent African origin (RAO) model than to the multiregional evolution (MRE) one. Signs of population expansions in human mtDNA have seemed to confirm the RAO model [albeit in a modified “weak” form that suggests multiple bottlenecks and then expansions; Harpending et al. (1993)], as the African expansion seems to clearly pre-date the Asian and European ones. These signals have been seen as indicating the rise of modern humans in Africa and their subsequent expansion into the other continents.
It is now routinely assumed that such signals of expansions support the most controversial of the claims of the strict RAO model—that all non-African “archaics” were replaced and all living people are descended exclusively from African modern humans (Manderscheid and Rogers, 1996). For this to be true, the entire extant human genome has to be derived from recent Africans. Therefore, if the signals of expansions in mtDNA, for example, indicate a population history rather than merely the history of a single genetic locus, the same signals should be discernable at all genetic loci.
Others have proposed models intermediate between the strict RAO and MRE models (Smith, 1985, Relethford, 2001 and Templeton, 2002). Relethford called his version “mostly out of Africa” because in it there is actual movement of populations from Africa. These newly arrived Africans mostly replace the local archaics, but there is some degree of admixture. On the other hand, in our model, there is no long distance movement of populations at all; change is driven entirely by local gene exchange among demes and natural selection. This model has the advantage of parsimony and simplicity, and it will be important to disentangle the effects of selection and long range migration from the archaeological and fossil records. For example, if there were long range population movements with local hybridization, then signatures of that hybridization should persist and be discernible in the fossil record and in populations today. In contrast, our model posits that there are hybrids essentially only at the wavefront. Since this front is moving at something more than 3 km per generation, it would take about 30 generations, or 750 years, to travel 100 km. We would then expect to find hybrid-looking fossils only within this small temporal window.
Templeton's (2002) paper was an ambitious attempt to trace ancient gene flow from molecular markers. He examined the geographic distribution of subclades of several markers with an intuitively appealing logic that allowed him to date major movements to and from Africa. There are, however, several problems. His algorithm is regarded with skepticism by population geneticists (Felsenstein, 2003). Moreover, even if his algorithm were to identify real movements between ancestral populations, there is no information about where those populations were at the time. For example, a signature of movement between African and Asian ancestors several hundred thousand years ago might have been a movement between Africa and Asia under MRE, but a movement between adjacent river valleys, for example, under RAO since those ancestral populations would have been in Africa at the time. Templeton's findings provided almost no evidence for distinguishing among models of modern human origins.
A strongly negative value (e.g., ≤ −1.5) of the Tajima D statistic (TD; Tajima, 1989) for a single locus likely indicates a selective sweep at that locus, while many such values obtained at independent loci would suggest a population expansion. Przeworski et al. (2000), analyzing data from 16 independent loci, found nearly evenly distributed positive and negative TD-values, thus offering no support for putative population expansions. Stephens et al. (2001), analyzing data from 313 genes, found that 90% had negative values, but only a fraction of these were statistically significant.
In the RAO model, all loci should have strongly negative TD-values, comparable to that shown in non-African mtDNA [TD = −2.28; Ingman et al. (2000)]. Thus, the nuclear data do not consistently signal expansion, and when they do, the signal is of a mild expansion, perhaps reflecting only post-Pleistocene population growth associated with the spread of agriculture.
Alternative explanations for the puzzling features of the genetic data discussed above may be found in a recently proposed theory of modern human origins. Arguing along the lines of Sewall Wright's (1932) “shifting balance” theory, Eswaran (2002) suggested that the African transition to anatomical modernity may not have been a speciation event, but was rather a “character change” involving alleles at multiple loci that cooperated to confer a co-adapted genetic advantage to modern humans. Given small random movements of hunter-gatherer groups (demic diffusion), and under the condition of a low rate of interbreeding between modern and archaic humans, such an advantageous gene combination could spread as a wave of advance, or a “diffusion wave,” of anatomical modernity (Eswaran, 2002).
One can visualize this process as that of the region of modern humans expanding at a steady rate into the region of archaic humans, the two regions being separated by a moving “wavefront” where the modern and archaic populations overlap. Only at the wavefront would both human types coexist; therefore, all hybridization and all selection favoring the moderns against the archaics—and thus all expansions in the modern population—would occur there.
According to this theory, the progress of the wave could be accompanied by considerable hybridization at the wavefront. Even so, the assimilation of archaic human genes into the modern populations would be low if the advantageous modern gene combination were complex enough that hybrids, with no selective advantage from their incomplete complement of modern genes, rarely became fully modern. Under such circumstances, the wave would essentially be an expansion of the modern humans at the wavefront. Further, as the small wavefront modern population would at any time be principally derived from previous wavefront moderns, the wavefront modern population would become severely bottlenecked over the thousands of generations that the wave took to travel from Africa to the far corners of Asia and Europe.
However, as all new modern populations would be created principally by the small wavefront modern population, the bottleneck would be followed by a continuous “rolling” expansion in the wake of the wave. As the signs of the wavefront bottleneck and the subsequent expansion would be passed on to the emergent modern populations, this theory offers an explanation for the bottleneck-and-expansion signature seen in so much human genetic data. It also explains why the expansions in Asia and Europe could have occurred tens of thousands of years after the African one (Harpending et al., 1993), for the wave would have traveled at about 3 km per generation, given the empirical evidence of the spread of modern humans.
Under conditions of a limited rate of archaic assimilation, only a few polymorphisms would survive at each locus in the bottlenecked wavefront modern populations. So, it is possible that African alleles often spread with the wavefront across the world. Such loci would then show signs of an expansion of a previously small set of African polymorphisms into a worldwide population. However, given a non-zero rate of assimilation from archaic populations, it is also possible that the wavefront moderns would, at some point along their spread, assimilate archaic human alleles (at loci unassociated with the functional advantages of modernity), which would then “surf” the wavefront and spread along with anatomical modernity. Thus, at these loci, the final modern world populations would have African/“modern” alleles, as well as alleles assimilated from archaic populations. The latter loci would show a considerable time depth and a corresponding lack of signs of expansions. This seems the most plausible explanation for the inconsistent signals of expansions obtained from various STR statistics (Eswaran, 2003), as well as the weak and variable signs of expansion in humans nuclear SNPs and the correlation among loci between Tajima's D and nucleotide diversity (Stephens et al., 2001).
Missing signs of expansions at many genetic loci would be correlated with assimilation at those loci from non-African archaic populations. Such assimilation would obviously also be compatible with evidence of great time depth in present-day non-Africans and of ancient and uniquely non-African polymorphisms (Harding et al., 1997, Harding et al., 2000, Zhao et al., 2000, Yu et al., 2001 and Yu et al., 2002). It would also explain why significant geographical structuring (presumably ancient, and with partly archaic roots) is often seen at such loci, but not in others like mtDNA. The theory thus suggests that present day modern humans are not exclusively derived from early modern Africans, but have a significant genetic inheritance from non-African archaics as well.
In this paper, we explore this proposed scenario through simulations of a modified version of the numerical model of Eswaran (2002). We use the model to compute population statistics of the emergent modern populations for two cases simulating (a) the spread of modern humans from a regional source across a one-dimensional world through the replacement of archaic types, and (b) the analogous spread of a modern human type defined by an advantageous combination of some C unlinked genes. We show that while the replacement case reproduces some of the gross features of the genetic data, the model replicates its subtler details only in the assimilation case—thereby arguing that significant assimilation from non-African archaics accompanied the modern human transition. Our model is the simplest implementation of the idea of a coadapted gene complex, a phenotype, and the consequences for the neutral genome of a selective phenotype sweep.
The question immediately arises as to how widespread was archaic assimilation in the human genome. Even a rough estimate suggests that assimilation was surprisingly high—surprising because the debate until now has been whether there was any assimilation at all. The simulations conducted here have shown that significant TD-values are strongly correlated with low assimilation, and conversely, that loci with high assimilation usually yield non-significant (but often negative) TD-values.
The Tajima D statistic is ideally suited for detecting assimilation from archaic populations. Given the long history of humans living outside of Africa, there would have been significant geographical structure (which increases TD) in the global human population at the time of the wave initiation, ca. 100,000 years ago. Thus, any assimilation from non-African archaic humans would inevitably increase TD, reducing the possibility of a significant signal of expansion. Therefore, TD is less likely to show expansions than other statistics if assimilation occurs. [See Yu et al. (2002) for a possible case in point.]
We can make a stronger assertion based on a comparison of nuclear loci with mtDNA. The deep differences between Neandertal and modern mtDNA, and the extremely low variability and geographical structure in modern mtDNA leaves little doubt that archaic mtDNA was largely, if not completely, replaced. The empirical TD for mtDNA in non-African populations is −2.28 (Ingman et al., 2000). While such a low TD-value is not obtained in the simulations of 10,000 individuals that we described above, it is well within the range of TD-values obtained for simulated world populations of 30,000 or 50,000.
Recovery from the wavefront bottlenecks in these larger simulated populations leads to stronger signals of expansions, i.e., more negative values of TD, even while the effective populations indicated by the mean pairwise differences remain below 10,000 at the simulated present day (as the pairwise differences have not fully recovered their equilibrium values after the wave). These latter simulations are, we believe, closer to the putative modern human diffusion wave, as they deliver highly negative TD-values in the range empirically seen in mtDNA. However, the TD-values for the replacement cases in these larger simulated populations nearly always fall within the 90% significance range (TD ≤ −1.5). This suggests that any loci with empirical TD-values that are less than 90% significant are likely to have been affected by assimilation. For example, the “geography-based” sample of 437 loci presented by Ptak and Prezeworski (2002) shows fewer than 25% of the values are below −1.55, implying, by the above argument, that around 75% of the loci had significant assimilation. These are astoundingly high figures.
Other data, too, suggest pervasive assimilation. Scans of 624 STR loci by Storz et al. (2004) revealed that 13 of these had significantly reduced variability by their very strict criterion, which the authors attributed to selection, but which we think signals “replacement” loci. Even among the 13 loci, reduced variation occurred either in Europe or Asia, but rarely in both—which seems peculiar if selection were involved, but is entirely likely if random fixation of certain alleles carried by the wavefront independently occurred in the separate Asian and European waves. Only one of the 13 apparent sweeps was seen in Africa, where the diffusion wave model predicts some sub-Saharan populations would not have been subjected to the wave. Therefore, we believe the STR pattern better fits the diffusion wave hypothesis than the selectionist one. By looser criteria, approximately 25% of their loci showed this pattern of reduced variability outside of Africa—in either Europe or Asia, but not both. While Storz et al. (2004) proposed that the patterns are due to selection, it is important to note that they studied STRs with no known functional significance.
The immediate objection to the possibility of such pervasive assimilation in the nuclear genome may come from physical anthropologists. If such a degree of assimilation occurred during the modern human transition, they may ask, why did the modern human morphology remain essentially the same across the world, rather than showing physical signs of admixture with archaics from Asia and Europe? One possible answer to this question has already been given by Eswaran (2002), who argued that the modern morphology itself may have given the coadapted modern advantage—possibly due to reduced childbirth mortality—that propagated modernity. Thus, the modern morphology, and the alleles that “coded” for it, could be fixed in all modern populations even while the rest of the human genome carried a considerable number of assimilated archaic human alleles. Other aspects of modern human morphology could also have been selectively advantageous, but it is not immediately apparent what they could have been. Some correlated aspect of energy requirement and usage might be involved.
With the exception of the C loci associated with modernity, the simulations presented here consider only neutral loci. Thus, the interpretation of the contrasting signals of expansions may be thought to hold only for such loci. To take an extreme view: is it possible that assimilation from archaics affected only neutral parts of the genome, while the functional parts were entirely derived from early modern Africans?
The evidence weighs heavily against this possibility. Many, even most, functional loci globally surveyed (e.g., β-globin, MC1R, PDHA1, Dys44, Y-chromosome, etc.) show deep structure both geographically and temporally, with coalescence times for non-African variation extending to much earlier time periods than the first emergence of modern humans in Africa. This strongly suggests that archaic assimilation affected these loci. The TD values, too, are usually non-significant and even positive, not even remotely suggesting population expansions. Moreover, in functional loci, an expansion would cause strongly negative TD-values in a random mating population, except in cases where deep phylogenetic structure was preserved by balancing selection before the expansion. Two of us (HCH, ARR) proposed balancing selection as an explanation for the lack of signals of expansions at functional loci (Harpending and Rogers, 2000), but such loci do not show some other signs of such selection (Wall and Przeworski, 2000). On the other hand, assimilation from archaic humans is a sufficient explanation for the missing signs of expansions, especially since loci with local selective advantage are more likely to be assimilated (Eswaran, 2002), and loci under balancing selection are also more likely to be assimilated.
The simulations presented here suggest resolutions for a number of crucial puzzles in the genetic data on modern human origins.
A diffusion wave of a complex genotype can explain why mismatch distributions of high-mutation-rate loci (such as mtDNA) show late Pleistocene expansions, while those of lower-mutation-rate SNPs show a contraction (Marth et al., 2003). It also explains why the more rapidly responsive site frequency spectra of SNPs show a bottleneck-and-expansion history (Marth et al., 2004). These explanations follow directly as consequences of a low assimilation-rate diffusion wave of moderns spreading out of Africa.
The same mechanism also explains why the expansions in Europe and Asia followed so late after the expansions in Africa (Harpending et al., 1993, Reich et al., 2001 and Gabriel et al., 2002), while certain populations in sub-Saharan Africa show no signs of expansions (Excoffier and Schneider, 1999). The model suggests that these populations are directly descended from the first modern populations in the “core region,” which would not be swept by the wave (Eswaran, 2002). But perhaps the most interesting explanations offered by the model concerns why—even among non-Africans—certain other loci do not show the characteristic bottleneck-and-expansion pattern and why, while most show mildly negative Tajima D values, there is so much variation in these values. These empirical findings directly suggest that assimilation from archaic human populations accompanied the modern human transition across the world. The bottleneck at the wavefront, while greatly restricting the genetic diversity in the non-African (and north African) modern populations, randomly allowed—at least at neutral loci—either African polymorphisms to spread worldwide, or else allowed non-African polymorphisms to be assimilated and spread along with the wavefront. In the first case, we see strong signals of expansions, as in mtDNA; in the second case, we see less clear-cut signals of expansions, often accompanied by signs of deep population subdivision, significant numbers of unique non-African polymorphisms, and great time depths in non-African populations. The latter signs have been found in numerous nuclear loci studied in the last few years. We conjecture that as much as 80% of the nuclear genome is significantly affected by assimilation from archaic humans (i.e., 80% of loci may have some archaic admixture, not that the human genome is 80% archaic).
While each locus has its own history, the above reasoning suggests that African-dominated loci would all roughly tell the same story, while the others would each have its own—for assimilation would have varied in time and place in each case. Thus in the late 1990s, after a decade when most geneticists became convinced of the strict replacement recent African origin model, there was confusion when many nuclear loci—each in its own way—contradicted the patterns first seen in mtDNA. Yet, the following of that particular model remained strong, as there was no other theory that could explain the contrasting patterns. Now there is such a theory, and it tells us that while modern humans first emerged in Africa, living human populations carry within them a substantial genetic inheritance that had its origins in non-African archaics.
Sons, daughters and professions
Not much time, but I wanted to link to this blog entry which reviews the recent paper by Kanazawa and Vandermassen which surveys 3,000 individuals and finds a strong tendency for people in "systemizing" professions to have sons and vice-versa for those in "empathizing" professions. If you want a "pulse of the public" (or high schoolers posing as programmers) check out this thread at Slashdot.
Addendum: I have heard from animal science people that a variety of alterations in the equilibrium of chemicals in semen can shift the XX:XY balance greatly.
Related: Previous post on this paper.
Of course, math doesn't mean that evolutionary biology is a bon afide "hard science" (see economics),1 but evolutionary biologists rely both on ecological observation and experimental breeding to test and explore their theoretical models (not to mention the genomic revolution, etc.). Where molecular biology is a "hard science" because of its relentless empirical reductionism, evolutionary biology is a duet of theory and data in the best tradition of science. I have asserted before that emphasizing natural history2 (morphological change) over the underlying processes (selection, drift, mutation, etc.) tends to skew public perceptions about evolutionary theory, and leaves it as a "just-so" hypothesis in the minds of many. My suggestion was that a more thorough, or at least transparent, grounding in microevolution to compliment macroevolution would reminds the public of the real processes that drive evolution as opposed to the flashy outcomes (flashy when evaluated over geological time scales). Perhaps there would be fewer demands to see "speciations involving gross body plan alternations in a few generations." The fact is that microevolution and macroevolution are on a continuous spectrum and the separation of one from the other is an artificial human construct. Even "pluralists" who argue for multi-level selection would probably concede the artificiality of any attempt to erect a high wall between the two levels of study. Macroevolution and microevolution kiss each other at the level of the species, and it can be argued that species are the only "real" taxonomic category in the Linnean system, yet even its bounds and definitions are subject to dispute. Though most Creationists and Intelligent Design proponents admit the reality of microevolution, it is too often an afterthought, and concepts like speciation get decoupled from the genetical dynamics which undergird differentiation (for example, the genetic divergence that occurs after geographical isolation, and the possible incompabilities that emerge out of disparate genetic backgrounds).
RPM offers that even the Hardy-Weinberg equation is hard going for many undergraduate biology majors. This is fair enough, but life is often easier when you don't derive anything and simply offer a few basic formulae to illustrate general concepts. So I am thinking the Hardy-Weinberg equation, the breeder's equation or one of the equations that gives one a sense of the power of random genetic drift. Students today are primed to memorize rather than understand equations, but even the minimal consciousness of the quantitative structure holding up the squishy semantically amorphous concepts would likely be beneficial.
1 - Fisher and Haldane received their bachelor's in mathematics. J.M. Smith was trained as an engineer. Richard Lewontin has a master's degree in mathematical statistics. Also, on the point about economics, I do not mean to imply that it is not difficult, rather, I mean to imply that there are difficulties with testing economic theories. In many ways microeconomics and microevolution are sister disciplines, but natural scientists can test their models on worms and bacteria.
2 - I do not mean to minimize Natural History. Many evolutionary biologists would not be evolutionary biologists if it were not for Natural History, just as many physicists would not be physicists were it not for Astronomy. The key is that the grand questions and panoramic vistas offered by these historical and sensorally rich disciplines must often be explored via more reductionistic methods. Since I have stated that science ~ method, it makes good sense that the public should be more aware of the existence and importance of the methodological (technical) disciplines.
May 22, 2005
Why no white aboriginals?
John Hawkes reviews a Jared Diamond review of some literature on the evolution of human skin color variation. It seems plausible that on a world-wide scale skin color variation is a reaction to a variety of environmental selection pressures, relaxation of functional constraints and social/sexual selection. Diamond focuses on the idea that balance of catabolism of folate and synthesis of vitamin D as a function of ultraviolent radiation (UVR) exposure is the primary determinant. But then he asks, what explains the dark skins of Australian Aboriginals and Tasmanians? In The Third Chimpanzee Diamond opined that sexual selection, not enviornmental selection, was the primary factor in diversifying human skin coloration. This was a qualitative assertion, and I do not not believe it has stood the test of time, seeing as how a strong positive quantitative correlation between UVR levels and melanin levels as well as evidence that purifying selection has been operative amongst these same dark skinned peoples in maintaining a low diversity on the MC1R locus both suggest long-term environmental selection (it being the central nexus in the regulation of melanin production).
The Australian Aboriginals are the great exception, and their extinct Tasmanian relatives were the specific example that Diamond noted when he offered that sexual selection was crucial, as these peoples remained dark skinned even after 10,000 years of isolation in their cool cloudy island home. John suggests that the low genetic variation common among island peoples might be the factor behind why the folks of Oz remained dark. Certainly in the New World there is some variation in skin color among the indigenous peoples, but the tribes of the north remained far darker than equivalent Old World groups (and similarly those of the equatorial regions do not rival Africans, South Indians or Melanesians in complexion). This suggests that the genetic background does matter.
Nevertheless, in the case of Australia proper, I suspect that the problem might have been less the isolation, than the fact that there was a fitness barrier over which alleles for lighter skin could not cross (note that Dingos only arrived in Australia over the last 5,000 years, so I suspect that some people did stray into Australia now and then as well). That is, the reservoir for alleles for lighter skin in eastern Eurasia would have had to have been passed from population to population across the archipelagos of Southeast Asia and likely via Papua New Guinea. Of course the relatively light complexions (in comparison to Melanesians) of the peoples of Polynesia suggests that such alleles could "hitchhike" with culturally adept folk. How likely would this have been over the ~40,000 years of human habitation of Australia? How about mutations for light skin?
In any case, what ever happened to those blonde Australian Aboriginals? Was that all the result of admixture? Internet searches come up blank, though C.S. Coon seemed to discount that they were byblows of Dutch sailors.
Related: Julian David has pointed out that much of Australia is tropical, and Tasmania is at the same latitude as Corsica. This is a fair point, but at the latitude of Corsica Eurasians generally have brunette white or pale olive skin. Still many shades fairer than the condition of the Tasmanians.
A new study pinpoints a polymorphism on the androgen receptor gene (AR), located on the X chromosome, as the primary factor in early male pattern baldness among German men. The authors also postulate recent selection for this gene.
Chess & the ladies
Today, I stumbled on to this: ARE GENDER DIFFERENCES IN HIGH ACHIEVEMENT DISAPPEARING? A TEST IN ONE INTELLECTUAL DOMAIN (that domain being chess). The authors conclude that there has been little convergence in the sex ratio at the higher ends, Judit Polgar aside.
Chess isn't something that was present in any hypothetical EEA, though the usual suspects predominate, so I won't speculate on what the biological, psychological and social variables are that result in success in that field. But, it seems any attempt to simply assert that nebulous "social pressure" is the cause of the imbalance has to control for geekitude. If those who feel that sexual equalitarianism in fields like chess and the physical sciences are among the great pressing concerns in a world where burquas and beatings are common place, I really want them to outline their model of "Geek Reducation Camps" where young XX minds are cleansed of their excessive focus on interpersonal skills, bodily hygiene and less than monomanical enthusiasm for esoteric cognitive domains.
It seems that the proponents of sexual equalitarnism in outcomes play a bait and switch: on the one hand they will admit that both biology and sociology play a role, but we should attempt to level the playing field and see where chips may fall. The problem occurs when the chips don't fall the way they want them to fall. Instead of "let's remove barriers to female entry," there is a shift toward "let's make this more 'female friendly,'2" and if that isn't possible, "let's give women a 'space of their own.'" The ball keeps getting kicked around in their attempt to enforce parity until you realize that the aim here is basically social reengineering and manipulation of groups, not the opening up of opportunities for individuals.
1 - I await the "All-Gentiles National Chess Championships."
2 - The idea that something needs to be 'female friendly' makes one wonder if a) females have average biases which need to be considered or b) there is a wider scale program at work of not just equalizing males and females, but reworking the norms of society as a whole.
In The New York Times today there is an article that highlights the trend of increased evangelical enrollment at Ivy League universities. There is a folk-anthropological feel to the whole piece, and I found it interesting that the author states that Calvin College is "an evangelical institution." Specifically, Calvin is an institution that derives from the Reformed tradition of Protestant Christianity (as the name Calvin should emphasize). This subtly is irrelevant to most readers of The New York Times, but of more interest to the general audience is the fact that 1/3 of Calvin College professors recently signed a letter saying that disagree with the President's policies prior to his arrival to make a commencement speech. My point is that terms like "evangelicals" are used very sloppily by most in the establishment media because of their unfamiliarity (and disinterest) in the nuances that a wide swath of America takes very seriously. The term "evangelical" as understood by many right-thinking liberals connotes a generally "backward" and conservative worldview, so a story that chronicles the emergence of an evangelical upper middle class and its entrance into the Ivy League has a "ain't that somethin'" feel. These articles add little to the readership's base of knowledge, and don't disrupt the standard model of the target audience by injecting surprises, such as the fact that the rise of evangelicalism in academia in places like Harvard is strongly correlated with the prominence of Asian-American Christians, or that perhaps evangelicals who attend and graduate from Ivy League schools might not be your run-of-the-mill believer. Remember, Princeton was founded in part as a low church proto-evangelical Presbyterian alternative to Harvard and the other New England Ivies, who had abandoned orthodox Christianity (many had Congregationalist or Baptist origins) by the late 18th century, but in its turn it became absorbed into the elite milieu and shed its own sectarian past.
Commentary on Koranaltry
Randall Parker has a wide ranging post reflecting on the response to the "Koran flushing" incident. Aziz Poonwalla argues that the Koran abuse was only a trigger for underlying rage. Part of the problem of course is that stories like this range over multiple countries and several layers of analysis get confounded together.
Baron-Cohen on systemizers, empathizers and assortative mating
Simon Baron-Cohen has a new piece over at Edge elaborating on his ideas about systemizers and empathizers. He received many responses and responded to those responses.
I think there are two primary issues that I see here:
The most accurate model that explains human psychological variation along the axis of sex (and beyond) mixes genetic biases and a developmental arc that is both biologically (hormones, nutrition, etc.) and socially mediated. The scholarly 1 argument is generally over the details. The empirical data on the ground is mixed, and seems (to my eye) be bogged down by semantic cross-talk. For example, Baron-Cohen's systemizer-empthaizer spectrum quickly becomes depicted as a typology by one respondent, to which he replies that he perceives it as a spectrum. But of course verbally he can't simply refer to a numerical point on his spectrum and assume he'll be understood, he has to decompose the range of variation into two categories. This is why Baron-Cohen likely placed spare normal distribution graphs on many pages of his book The Essential Difference, verbally he had to speak in categories not to be bogged down in stat-jibberish, but quite clearly he does not conceive his model in a typological fashion in its essense and wanted to remind his readers of that reality graphically.
Another point, which Helena Cronin's response zooms in on, is that there are a priori considerations as to why human males and females should display a wide range of phenotypic median differences. This is a crucial point that I think many who operate outside the natural sciences, in particular evolutionary biology, miss. Sex is an evolutionary mystery. Any given parthogenetic (asexual, virginal procreation) individual would generate twice as many copies of their genes (two alleles instead of one) with each gestation as a female who exchanges genetic material with a male. Additionally, the existence of the male sex, which itself does not gestate, seems very wasteful. The short of it is that in terms of adaptation sexual reproduction must increase the fitness of said sexual individual by at least a factor of two over asexual reproduction. There have been many explanations of sex, and many hypotheses for why males exist, most of them starting with the position that sex facilitates faster evolutionary response to selection via an increase in variation (recombination and allelic exchange). Additionally, the high possible reproductive variance of males means that they can act to dampen down the genetic load of a population due to a correlation between fitness and fecundity in every generation (so that unfit males with high mutational load act as carriers of deleterious alleles into evolutionary oblivion). Some people appeal to structural constraints, that is, sex exists in higher animals because of the phylogenetic past of these species or genetic competition between cytoplasmic DNA (there are parthogenetic insects and what not, so I am skeptical of this). But even if sex is a structural holdover from our past, it is a background condition against which animals must compete and evolve.
Sexual dimorphism is a reality in human beings. Regardless of the origin of sex, humans have been stuck with the fact ~1/2 of the species can not gestate and bring forth offspring, and this will have evolutionary consequences (though more slowly than usual). This compelling background assumption makes the theories of individuals like Simon Baron-Cohen much more intelligible, and invidious accusations of political motive can take a step back. I suspect this explains two primary forms of response to Baron-Cohen's hypothesis: No, you are wrong, and, probably wrong, but here are other options and possibilities. Some people are aware that something needs to be explained outside of cultural shaping (because sex differences precede the emergence of human culture in other animals, so parsimony suggests that there is a biological aspect to it), while others seem to wish away this reality.
Related: By now you have probably noticed that Steven Pinker and Elizabeth Spelke debated sex differences in the mind, but check out the responses.
1 - There are some on the traditionalist Right who welcome the findings of evolutionary psychologists because it buttresses their own moral normative positions. But the reality is that usually these positions are solid and live without fear from biology because they precede scientific empirical data. Therefore, a mapping of biology -> ideology must always be examined in light of the factors involved in the "->", as opposed to simply assuming that the connection is transparent, as many on the Right do. And, as many on the Left do, for the opposition to biologistic thinking tends to issue from a naive understanding among those who style themselves "progressives" about the possibilities that are constrained by the progress of science. The reality I would argue is that constraint is a condition of human existence, and the constraints suggested by science are more than counteracted by the possibilities and new avenues of exploration opened up.