Sunday, April 30, 2006
Via Dienekes I found this important new paper on Finnish genetics, Regional differences among the Finns: A Y-chromosomal perspective. This is a meaty paper, so I put it up in the GNXP forum files ("finnY"). Here is the abstract:
Points of note.
1) mtDNA and Y lineages often give different results. As the paper emphasizes this may be because of different population histories (e.g., Mestizos tend to exhibit Western European Y chromsomal profiles and Amerindian mtDNA because of their ethnogenesis), or, it may be because of sociological dynamics (patrilocality tends homogenize mtDNA distributions while fostering local Y substructure). Other factors like selective sweeps on mtDNA could also result in a difference.
2) There is a east to west gradient in markers. This shouldn't surprise too much. About 10% of the variation was accounted for by this population vs. population difference (80% was intragroup, while 10% was between groups within the subpopulation).
3) I've noted before that R1b, which is modal in much of western Europe, is rather rare in Finland (and is found in moderate frequencies in Sweden). Also, M17, which is associated with Slavs in a European context, is also found at moderate levels in Finland (M17 in England seems to be associated with settlement in the Danelaw by Norwegians and Danes).
4) I am a bit confused as to whether these data included Finns of Swedish ethnicity.
5) The authors note that they do detect the signature of migrations to areas where there is recent attested resettlement by Finns from a particular locale.
6) The authors reiterate findings that the Finnish Y lineages show no evidence of some found at high frequencies in Siberian groups which also carry the common Finno-Ugric Tat C marker. In other words, we can probably eliminate the possibility of a recent admixture event with a Siberian group to explain the peculiarities of the Finnish Y chromosomal profile (either the Siberians received Tat C from Finland, or, I think more likely there are particular similarities amongst the circumpolar peoples of Eurasia which have a deep time depth before their later diversification and admixture).
7) The nonrecombinant portion of the Y chromosome has a lot more sequence to analyze than the mtDNA. This gives researchers more information to work with, but, my understanding is that the molecular clock is far less precisely calibrated than on the mtDNA, so the time frame tends to be sketchier.
Overall, this paper reinforces the idea that Finns are distinct from the peoples of Western Europe, seeing as they have little evidence of R1b, but that they share considerable continuity with other Scandinavians, as well as peoples to the East (Slavs). One issue that I think needs to be addressed is that the mental model people have in regards to the genesis of the Finns is often of a group of Siberian tribes hurtling through "Slav space" and settling amongst a bunch of Scandinavians and slowly admixing. I think it is easy for people to imagine "clumps" of populations in a larger distinct matrix, and then model the mixture of clumps resulting in the peoples we see around us. I suspect that the reality is that many of the genetic gradients are the result of more prosaic deme-to-deme mate exchange and movement over time. Large migrations might have played a role, but the introgression of M17 into Finland (if it wasn't indigenous to Finland in the first place) need not be explained by a few movements of Slavic tribes, rather, it might have been due to the long term residence of Slavs along the southern edge of the Finnish world and the inevitable bleeding over of marriage networks.
In any case, the paper has a lot of historical context and conjecture, and I'm curious what some of the Finnish readers think about those points.
Purely out of sociological interest, here is a picture of Britney's crack. (That got your attention, didn't it?)
You may not be interested in Big Pharma, but Big Pharma is interested in you.
PLoS Medicine has an issue on the pharmaceutical industry's disease mongering. I liked this article on serotonin & depression, namely the disconnect between the muddy consensus within neuroscience (it may or may not be somehow involved) and the boastful direct-to-consumer advertisements (if you're depressed, you've probably got low levels of stuff we're happy to sell you). Given how little we understand about the brain compared to other organs; given how little we understand of the long-term effects of brain drugs; and given that we have recent evidence that -- prepare to be shocked -- Big Pharma honchos will try to keep harmful side-effects under wraps lest their profits suffer; I'd say it's a good bet to stay away from the stuff.
That raises the question: should we keep others from using such things as well? It's their body and their money, correct? Yes, but under the present circumstances, a good case could be made against their use -- namely, that they wouldn't have seen a doctor and asked for medicine had not the PR & advertising industries knowingly mislead them as to the status and/or cause of their condition. Again, this is crucial if they're being mislead as to the long-term consequences, which are potentially great when we're talking about drugs that affect an organ we understand poorly. Since it's easier to screw up a complex system than to improve it, we should adopt that as the null hypothesis for brain drugs, which only longitudinal studies could disconfirm.
Now, if the disease were life-threatening, like liver failure, you could argue that if the patient consents, dire measures could be taken -- after all, they face imminent death in any event, and basic work (where doctors will break some eggs) is needed in order to fine-tune the art of liver transplants before they become safe. In such cases, maybe. But anxiety and depression, let alone the conditions treated by "lifestyle drugs" such as Viagra, are not in the same league as liver failure. Moreover, you could make a similar argument to one for closing up most plastic surgery offices: that is, they represent a failure of the market to allocate resources where they're needed. The smartest, most highly motivated doctors should be where health is lowest (mainly the elderly and poor), not making Orange County housewives look like space aliens with shotput boobs.
On the other end of the spectrum in the PLoS issue, there's this review of Female Sexual Dysfunction from a feminist / social constructionist p-o-v. Typical of critiques against "reductionist" approaches, it gets some of it right but for the wrong reasons. She's right that FSD is mostly made-up by Big Pharma and that men & women are different, though not due to social forces but to different biology. If natural selection allowed the average female to have a sexual appetite equal to that of the average male -- say bye-bye to the advantage of female choice. Ditto for reliability of orgasm -- if it were as simple as the male version, any old bum could win her over provided his body was warm.
In any case, what do the readers think the best strategy is for keeping Big Pharma on a tight leash? Clearly, it's not rationally arguing the issue with them, as they already understand the shortcomings but don't care. So, some sort of force or threat of force is needed -- not physical, obviously. I should clarify: what can we do? Surely the FDA could enact harsh measures, but they've proven to be wimps.
Friday, April 28, 2006
There's a hilarious, and often thoughtful, comment thread over at The American Scene. Ross Douthat is a Roman Catholic, and many of his readers are serious intellectual Christians. So, I am always interested when they object to the bizarre and obviously anthropogenic hocus-pocus of Mormonism. Some snips of interest:
Hear, hear! Now, Michael Brendan Dougherty:
There you have it!
Please note a point of irony, to some extent Mormon theology is materialistic. God is a being of flesh and bone, constrained by logic and the laws of the universe. Mormons need to make less recourse to bizarre semantic philosophical circumlocutions because their idea of God stays pretty close to our "cognitive machine code." This is the problem though, the Mormon god seems more like science fiction than supernaturalism because he is a creature of this universe more than a creator of the universe.
Related: One Nation Under Gods.
Is washed up 80s TV star Jan-Michael Vincent a Finnish adoptee? Note the similarity in appearance to "famous" Finn, Esa-Pekka Salonen. Suspiciously they both have hyphenated first names, and likely have had "grandfathers" who were made into cuckolds by Chinese sailors. Additionally, Vincent is a known drunk, a vice that Finns are all too familiar with. Raised by non-Suomi parents Vincent's genotype was subject to a different norm of reaction than might be have been the case in Finland. With its suffocatingly introverted and maladjusted culture Vincent might have flourished as a withdrawn curiosity. As it is, in the glamor seeking non-Suomi cultural milieu of the United States he withered under a harsh glare which evolution in the cool northern climes did not prepare him for....
Thursday, April 27, 2006
I was talking to Greg Cochran a few months ago, and we were talking about memory. Greg has described himself as having a "pack rat mind." I'm somewhat similar, all sorts of obscurities lurk back there, to show up periodically in the weirdest ways. But, I don't have a photographic memory, nothing close. People have asked me before if I have a photographic memory because I tend to remember details pretty well (I did weird things as a kid like memorize all the capitals in the world), but of course I knew very well my memory wasn't photographic. I've always wondered where the people with the photographic memory were, I'd have liked to meet them (I'd read about photographic memories in fiction of course). Anyway, this article in Slate offers a lot of evidence (or highlights the lack of evidence) that we should be skeptical about the idea of perfect photographic memories, or, at least that they are very very rare (as in 1 in millions). Also, reading Daniel Schacter's books makes me really wary of thinking of memory as a unitary cognitive process which we understand really well on a reflective level. Finally, those with a broad historical perspective will probably find the method of the loci of interest.
Wednesday, April 26, 2006
Tuesday, April 25, 2006
I predicted this is November 1998, yes I did Tony, you remember! Check out chunky Britney dancing.
I think I'm probably breaking some rule of blogger etiquitte by performing the dreaded fact-check manoeuver on Colby Cosh just after he linked to my other blog. But it always makes me wince when people I respect stake out strong positions where they're demonstrably wrong on the facts, so I'm afraid I cannot let this pass:
Africans aren't helpless animals--they know what works against malaria. Unfortunately, what works against malaria is DDT. But any country that proposes a program of household DDT application faces starvation at the hands of European bureaucrats and consumers. The nets are an unnecessarily expensive and epidemiologically phony sauve-qui-peut measure, a work-around for what could be described as the greatest ongoing mass murder ever perpetrated.
This is one of those strange memes that gets into the air and becomes part of the conventional wisdom, despite the fact that if you dig deep enough the whole thing turns out to be baseless. (Other examples include what Everybody Knows about the industrial revolution or the great depression.)
Cosh seems like he usually has pretty good bullshit detectors, and I would have thought that alarm bells would have started ringing when (if?) he noticed that one of the articles he cites was by Dr Rutledge Taylor, the man who directed the film 3 Billion and Counting. Hello there, lying with statistics! The film's site claims that "Africa loses nearly 3000 women and children on a daily basis ... to malaria alone".
But let that pass, and let's look at the allegation made against the EU. Let's see what the EU ambassador to the US has to say on the matter (emphasis mine):
The European Union has no objection to the safe spraying of houses with DDT for malaria control, but it does have concerns about illegal agricultural uses. The E.U., like the United States and 149 other countries that signed the Stockholm Convention on Persistent Organic Pollutants in 2001, believes that the use of DDT in agriculture should be phased out.
The "ban" on DDT is and always has been one on its agricultural use; household use is perfectly allowed. Here (PDF) we find, plain as day on the 4th page, that the "WHO recommends indoor residual spraying of DDT for malaria vector control." And there is a perfectly good reason for this partial ban: basic evolutionary logic suggests that injudicious use of a pesticide like DDT will tend to hasten the adaptation of the pests to the chemical, just as improper use of antibiotics has hastened the evolution of resistance in bacteria. And indeed this is exactly what has happened in some areas (PDF).
Saying that DDT "works" is like saying penicillin or erythromycin "works" -- yeah, for a while. But if you're not careful about it you can end up pushing your enemy to evolve faster. Like Derek Lowe says: "It's life or death for them. Just like it is for us."
Addendum: Tim Lambert has been covering this beat for a while, and most of my info on the subject comes by way of him. Anyone curious should read his full archives on the subject here.
Edit: I am a blithering idiot and somehow misread that as 300,000. I have no defense other than that this doesn't seem to square with the 3 billion figure that makes the title, but then they don't specifically say that those are deaths. This is an excellent lesson in the perils of firing off posts in a rush.
Edit the second: Aha! Now I know where I got that idea in my head. Apparently they did originally say what I thought they said, but then later changed the site after having this, er, discrepancy pointed out.
Edit the third: Lambert has more on the effectiveness of nets, which was the subject of Colby's original post.
Anyone know the best way to get a windows .exe to run within linux? I need to pass and retrieve some variables from a .exe which has an algorithm using the Asterisk pbx system (on the same box). Thanks.
Monday, April 24, 2006
I've developed a mild interest in East-West phylogeography in Europe in regards to human populations. In the process I stumbled onto this paper, Geographical heterogeneity of Y-chromosomal lineages in Norway. I've put the full PDF in the forum, here. Standard caveat, take this with a grain of salt!!! But, I've put some maps below that readers might find of interest.
Fig. 6. Multidimensional scaling analysis of pairwise Y-SNP based FST between 23 European countries. Data were gathered only from the geographical coordinates indicated. Map coloration is the result of algorithmic interpolation and must be interpreted appropriate skepticism.
Sunday, April 23, 2006
John Wilkins started a debate on race. I responded here & here. John responds to the response. Interesting discussion threads on Pharyngula, here & here. The Contingency Table adds his 2 cents. You all know about this topic, but I figured you might want pointers to the "discussion." I've stated at least twice that I'm an instrumentalist on this issue, here is the definition from Wiki:
For the record, I'm close to an instrumentalist on the "species concept" debate too.
Update: My last response to John's last response. Evolgen also offers his 2 cents.
In previous posts and comments I have mentioned Haldane's Dilemma, and I thought it would be worth looking into the subject more closely.
The short answer to the question, 'Should we worry?', is 'No'. But when was I ever satisfied with a short answer? The following is not intended as a casual read but (hopefully) a resource for those who are following up the subject via search engines. As usual, I claim no technical expertise in genetics, so don't take my assertions on trust. Links and references are provided for those who want to explore the subject further.
In a classic 1957 paper, J. B. S. Haldane estimated the number of generations of natural selection required to take an advantageous gene from rarity to near-fixation in a population. His headline conclusion was that it would normally take about 300 generations. More accurately, on average about one gene would be fixed in every 300 generations, so that if several genes were under selection simultaneously, the time required to fix each would be longer, but the number of genes fixed per unit of time would be the same. [Note 1] The total length of time required to fix T genes would therefore be approximately 300T generations. [Added: To avoid misunderstanding, I should have emphasised this last point. Haldane does not claim that every gene takes 300 generations to go from rarity to fixation. Suppose there is a long-established process of selection with a stream of 100 advantageous genes under selection at any time. Suppose each gene on average takes 30,000 generations to fix. If we take one of these genes at random, it therefore has a probability of 1 in 30,000 of being fixed in any given generation. But there are 100 genes to choose from, so the expected number of genes to be fixed in any given generation is 100 x 1/30,000 = 1/300. Equivalently, we expect on average 1 gene to be fixed in any 300 generations. This is what Haldane claims, based on his various assumptions.]
Based on the information available in 1957, Haldane estimated the number of gene differences between closely related species (not to be confused with the number of gene changes required for speciation) as typically about 1,000. It would therefore take about 300,000 generations for this amount of divergence to evolve by natural selection. Haldane thought this was broadly consistent with the fossil record, so he saw no 'dilemma'.
In the 1960s new evidence showed more genetic diversity within and between species than was previously assumed. It therefore became problematic that natural selection seemed either too slow to explain the observed diversity or too costly in mortality for species to survive. Hence the 'dilemma'. Motoo Kimura used Haldane's figures to support his own theory of molecular evolution, maintaining that a large proportion of change at the molecular level is not due to selection but to genetic drift. In the resulting debate geneticists picked holes in Haldane's analysis, and showed that in some circumstances natural selection could be much quicker than Haldane had claimed. (Haldane died in 1964, so he took no part in this debate.) By the mid-1970s it was generally accepted that Haldane's Dilemma was not a serious problem. [Note 2]
The issue was reopened in 1992 by George C. Williams in his book Natural Selection: Domains, Levels and Challenges, where he argued that Haldane's Dilemma had not been solved, but 'merely faded away, because people got interested in other things'. The subject has also taken a bizarre twist in recent years as Haldane's Dilemma has been seized on by Creationists as an objection to evolution. (Searching the Web for 'Haldane's Dilemma', a large proportion of the results will be Creationist websites. A key Creationist example is here, and an evolutionist response is here.) This raises a dilemma of a different kind, as there is a danger that anyone who takes Haldane's Dilemma seriously will be misrepresented as a crypto-Creationist, or misquoted to give support to Creationism. So just to be clear: I do not think Haldane's Dilemma is a major problem for evolutionary theory. On the other hand, I do think that George C. Williams raised some interesting points. The real value of the Dilemma is now not so much to set any firm limit to the rate of evolution, as to focus attention on important questions about how natural selection works...
Haldane's 1957 paper itself is available here. The arguments and calculations are not easy to follow, as the paper requires some prior knowledge of population genetics, and makes a lot of simplifying assumptions and approximations. There is also at least one serious misprint [note 3]. I will give my own outline of Haldane's argument, not always using Haldane's own notation.
First Haldane assumes that a population is in equilibrium with its environment, and that most members of the population have the best available genes (alleles) at most loci. Disadvantageous alleles are present at low frequencies (around 1 in 20,000 for dominants and 1 in 100 for recessives) due to a balance between selection and mutation.
The environment then changes so that some previously advantageous alleles are disadvantageous and vice versa. The newly disadvantageous alleles will each have a selective fitness detriment, s, relative to its advantageous alternative, where the s's may be different for each allele. Any individual lucky enough to have the best alleles at all loci has fitness 1 (by stipulation), while the bearers of disadvantageous alleles have fitness (1 - s)(1 - s)(1 - s), etc, with the appropriate s's for these alleles. Note that this assumes that the fitness effects of the alleles at different loci are independent, so that fitness is simply multiplicative. (If all the s's are small, fitness is also approximately additive, as the product-terms involving more than one s can be neglected.) This assumption of independent fitness effects is not discussed by Haldane.
Haldane assumes for simplicity that all selection occurs by way of mortality in the juvenile stage, i.e. before reproduction. If the population at the time of selection is N, and the frequency of a disadvantageous allele is q, there will be a certain number of selective deaths attributable to the allele in that generation, depending on the size of N, q, s, and the genetic characteristics of the allele (e.g. dominance). The selective deaths reduce the population size, but we assume that it is restored to N in the next generation, an assumption not discussed by Haldane [note 4]. In the new generation the frequency of the disadvantageous allele is reduced, while that of the advantageous alternative is increased. By iterating the process of selection, and assuming that the selective advantage remains constant, we can calculate D, the total number of selective deaths, expressed as a multiple of N, required to increase the frequency of the advantageous allele from rarity to near-fixation. Provided s is small, the problem can be approximately solved by integration. The technical part of Haldane's paper is concerned with performing these integrations for a variety of scenarios: haploid, diploid, partly recessive, sex-linked, and so on. The important conclusion is that over a wide range of parameters the resulting value of D does not vary drastically, though it is more sensitive to variations in the initial frequency q than in the fitness detriment s. For diploids D is usually between 10 and 100, with 30 as a representative value. This means that the total number of selective deaths required to take a single advantageous allele from rarity to near-fixation is about 30 times the population size. The process will therefore normally take at least 30 generations, but probably more: the best estimate remaining to be determined.
This problem is taken up in the Discussion section of Haldane's paper. The figure to be determined is the number of generations required for a single gene substitution. Call this K. As the total number of selective deaths required is about 30 times the population size, the number of selective deaths required per generation is about 30/K times the population size. However, usually more than one allele will be under selection at the same time. If each such allele involves d selective deaths per generation, then provided all the d's are small, so that there is no significant overlap in the selective deaths attributable to different alleles, their sum, Sd, is approximately the total of selective deaths per generation. (Strictly the d's and Sd are proportions of the population, rather than absolute numbers, but it is tedious to keep repeating this.) Since each gene substitution requires selective deaths totalling about 30 times the population size, Sd selective deaths can therefore be regarded as 'paying for' Sd/30 gene substitutions per generation. Equivalently, one gene substitution will on average occur every 30/Sd generations. But by definition this is also the desired number K, so we have K = 30/Sd. We can therefore estimate K if we know Sd. Here Haldane makes the assumption that the proportion of all mortality that is due to selection will usually be about 1/10, though occasionally as high as 1/2. (In most species under natural conditions, there are a lot of random, non-selective deaths, so Haldane's assumption is not unreasonable.) Taking 1/10 as typical, we therefore have K = 30/[1/10] = 300. Hence we get the headline figure of 300 generations required for a gene substitution.
Given the assumption that fitness effects are independent, the selective deaths which 'pay for' an increase in the frequency of one advantageous allele are neutral with respect to all other alleles. Provided the selective advantage for each allele is not very large (say, not more than 10%), there will be little overlap in the selective deaths which pay for different advantageous alleles, so that the cost of each allele must be paid in full by 300 generations worth of selective deaths. [Note 5] (Haldane does not spell this out, but it is worth making it explicit.)
There are obviously a lot of approximations and simplifications in all this, and Haldane himself mentions cases, such as colonisation of a new territory, where selection might be quicker than average. But given Haldane's key assumptions, his reasoning is generally accepted as sound. Criticism has therefore focused on the validity of the assumptions. A wide variety of objections and alternatives have been raised, some of which seem to me persuasive, others less so. A useful review in 1974 by V. Grant and R. Flake is available here. My own layman's assessment is as follows:
1. The weakest of Haldane's assumptions is that fitness effects are independent. This is crucial for his overall conclusions, so it is unfortunate that Haldane does not discuss it! A simple example shows how selection can be much faster with non-independent fitness. (I found this example in an article by Nick Barton and Linda Partridge, but they do not claim it as original.) Most of the cost of selection is incurred when an advantageous allele is rare. Suppose then that there are a number of rare advantageous alleles in a population. Suppose also that a proportion W of the population survives and breeds in each generation, and that all those individuals bearing any of the advantageous alleles are among the survivors. In this model all of the advantageous alleles will simultaneously increase to a frequency 1/W times their previous frequency in a single generation, so, for example, if W = 2/3, the frequency of each allele will jump to 1/[2/3] = 1.5 times its former frequency. There is no limit to the number of alleles that can be selected at this rate simultaneously, provided their total frequency in the population does not exceed W. In this simple model every selective death simultaneously helps pay for all the advantageous alleles, contrary to Haldane's assumption of independent fitness.
A somewhat more complicated model was examined by John Maynard Smith in a 1968 paper. In this model JMS assumes that all those individuals with more than an average number of advantageous alleles survive and breed, while all those below this threshold die. JMS finds that with this assumption, of the order of 1,000 times as many alleles can be selected simultaneously, for a given overall intensity of selection, as in Haldane's model. This implies that instead of on average 1 gene being fixed every 300 generations, there could be several genes fixed in each generation.
These examples suffice to show that selection much faster than Haldane supposed is possible. However, to show that something is possible is not the same as showing that it actually happens. One of George C. Williams's main arguments in reviving Haldane's Dilemma was that in practice the assumption of independent fitness effects was often a 'realistic approximation', and that more empirical research was needed into the actual patterns of selection. There may be some circumstances where Haldane's assumption of independent fitness is reasonable. There may be others where fitness is not independent but the pattern of selection is not as favourable to rapid evolution as in the simple models described above. In a critique of Maynard Smith's paper, P. O'Donald argued that a simple threshold model was unrealistic, and that it was more plausible that the fitness of a polygenic trait should be proportional to the square of its deviation from the optimum value. With a model based on this assumption, O'Donald found that selection could work somewhat faster than in Haldane's model, but nowhere near as fast as in Maynard Smith's.
2. In discussing Haldane's Dilemma a distinction is often made between hard and soft selection. As introduced and defined by Bruce Wallace, a hard selective disadvantage applies regardless of the density of population. Soft selection, on the other hand, does not apply until the population exceeds a certain threshold of density. It is argued that Haldane's model presuppose hard selection, and that it does not apply where soft selection predominates.
It is true that Haldane's illustrative scenario assumes hard selection, but his calculations would apply to any circumstances where the pattern of fitness satisfies his assumptions. Frequency-dependent selection might in principle do so. The real point of the soft-selection argument is that, according to Wallace, in soft selection the fitness of individuals is decided by their place in a rank order of fitness. At any given time there is a fixed number N of 'places' available for the population, determined by ecological factors, so that the first N individuals in order of fitness (allowing for random mortality) will survive, and the rest will die. It is evident that this is another version of threshold selection, as in Maynard Smith's model, and the same pros and cons apply.
3. It is sometimes suggested that Haldane's arguments do not apply to new advantageous mutations. A new advantageous mutation does not cause any deaths except to the extent that its bearers gradually squeeze out non-bearers (assuming a fixed population size). The maximum cumulative number of deaths caused by this 'squeezing out' can be no more than the total population size, and not 30 times the population size, as in Haldane's model.
I think this objection is largely misconceived. It is true that a new advantageous mutation cannot cause more individuals to die than the total population size, but it does require many more selective deaths than this.
To understand this paradoxical assertion, consider the following example. Suppose that in every generation 2% of a population dies from spells of extreme cold, against which the species has no defence. These deaths will be counted as part of random, non-selective mortality. Suppose now that a new dominant mutation gives its bearers partial protection against cold spells, so that only 1% instead of 2% of the bearers die from this cause. The bearers will therefore have a 1% fitness advantage over the non-bearers, and will gradually increase in frequency. During this process a large number of selective deaths will be attributable to the new mutation - usually more than 30 times the population size, because a new mutation probably starts from a greater rarity in the population than in Haldane's model. There are no more deaths from cold than before - in fact there are fewer - but deaths previously counted as non-selective are now selective.
So what? Does it matter if deaths are transferred from the 'non-selective' to the 'selective' category? If we are only considering a single gene, it probably does not matter, but if we are considering the overall scope for natural selection, it does. The problem is that there are only a certain number of deaths available to pay for natural selection. The number cannot exceed the total population size in any generation, and it will normally be much less than this, as there is bound to be a large amount of random mortality. The more mutations there are at any time, the fewer the deaths available to pay for each (assuming independent fitness). There is no free lunch: advantageous mutations still have to be paid for, and the 'funds' available, in terms of the scope for selective deaths, are limited. The problem is not that new advantageous mutations somehow make things worse - obviously not - but what they imply about the previous state of the species. If a large number of new advantageous mutations are under rapid selection, without any change in the environment, this suggests that the species was very badly adapted to its environment before. So how did it survive? One answer to this may be that the 'environment' of a species consists largely of other organisms - competitors, predators, prey, parasites, and so on - and they are all evolving together. At any given time a species may be adequately adopted to its organic environment, but if it does not keep evolving it will fall behind.
This may be true, but it does not seem particularly relevant to the case of strong selection of a large number of new mutations simultaneously. This would imply that the other species (competitors, etc) had somehow obtained a major advantage, so that the species under selection had to catch up. It isn't clear how this situation would arise.
4. An initially attractive answer to Haldane's Dilemma is that it only applies to selection due to differential mortality, and not to differential fertility. If some genotypes have more offspring than others, there is no need for selective deaths at all. The worst that can happen is that if there is a fixed population size, some individuals will be forced to have fewer or no offspring. But the cumulative total of individuals forced to be childless will not exceed the total population size. Selection by differential fertility is especially attractive when a gene is rare, because in these circumstances it is much less wasteful than selection by differential mortality. When an advantageous gene is rare, selection by mortality requires a fraction 1/x of the entire population to die just to raise the frequency of the small number of advantageous genes by roughly the same proportion (if selection is not very strong). In contrast, selection by fertility only requires the rare bearers of the advantageous gene each to have on average 1/x more offspring to achieve the same effect. This is much more efficient, from the point of view of the species a whole. Unfortunately, there is no reason to expect the evolutionary process to be efficient for the species as a whole.
Strictly speaking, Haldane's model does allow for selection by differential fertility. Haldane several times refers to diminished fertility as being equivalent to selective mortality. There is however an important difference. In the case of selective mortality, a certain number of actual deaths must occur. In contrast, 'diminished fertility' is measured relative to the fertility of the optimum genotype, which may be entirely hypothetical. If several advantageous genes are still rare, there will probably be no actual individual who has all of them. Whereas real deaths in any generation cannot exceed the actual population size, there is no upper limit to a hypothetical loss of fertility. Each new advantageous allele increases the fertility of the optimum genotype, against which 'diminished fertility' is measured. The 'cost' of selection may be largely theoretical. It does therefore seem that if we allow selection to be largely by differential fertility, there is no real constraint on the speed of evolution.
I think there is something to this argument, but that we should not be too optimistic about the scope for selection by differential fertility. The reasons for differences in fertility (number of offspring) of individuals in a species may be divided broadly into two categories:
a) differences in the resources the individual can devote to reproduction. This is turn depends on its general condition, and especially on its health and nutritional status;
b) differences in the number of offspring produced from a given amount of resources.
Differences of the first kind depend on much the same factors as differences in mortality, such as the ability to find food, to avoid predators, and to resist disease. They are therefore not really an alternative to selection by mortality, and differences in fertility of this kind, in so far as they have a genetic basis, are likely to be accompanied by selective deaths on much the same scale as in Haldane's model.
The second category of differences falls within the field of 'life history strategy'. There is a trade-off between the number of offspring produced and their average survival rate. We expect there to be an optimum fertility level for each species, determined by its ecology and behaviour. Any mutations which cause an individual to produce more offspring than the current optimum will in general be selected against, except in the special circumstance that the mutation itself changes the optimum, for example by increasing the efficiency of parental care. To expect it to be easy to increase fertility is to expect another free lunch.
5. A more technical criticism is of Haldane's measure of fitness. Haldane stipulates that the optimum genotype that can be formed from the available genes has fitness 1. But if some advantageous alleles are still rare, in a finite population the optimum genotype is unlikely to have any representatives, and the fitness of all existing individuals may appear very low by Haldane's measure. It has therefore been argued that fitness should be measured by reference to the best genotype available in practice. It is further argued that with this approach, the cost of selection is much lower, and that several alleles can be fixed in each generation, even if all the other assumptions of Haldane's model are adopted.
I have not followed all the details of this argument, but it has been used by some distinguished geneticists, such as Warren Ewens, so I am sure they have proved something. But I do not see how it can solve Haldane's Dilemma. Haldane's argument does not depend crucially on how fitness is measured. His key assumptions are:
a) selection is by means of differential mortality
b) selection at different loci is independent
c) selection at each locus is not very strong
d) there is a substantial amount of non-selective mortality.
From assumption (a) it seems inevitable that fixation of any single allele will require selective deaths cumulatively totalling several times the population size, and assumptions (b) - (d) entail that the cost of fixing more than one allele will be approximately the sum of the costs of fixing each. Setting a different benchmark for fitness would not help. I suspect that any findings to the contrary involve some de facto relaxation of the 'independence' assumption.
Overall, it seems to me that Haldane's Dilemma has more force than is sometimes assumed, and that it, or rather the issues it raises, should be taken seriously. Whenever it is suggested that a large number of genes have been under selection simultaneously, we need to look at what this implies for the intensity and mode of selection. This applies also when the selection of entities other than genes, such as social groups or cultural traits, is under consideration. For example, if it is suggested that cultural traits have evolved by the differential survival of societies possessing those traits, we need to take a hard look at what this implies for the number of group 'extinctions' and the number of cultural traits that might feasibly evolve in the way suggested.
At the same time, the Dilemma does not set a rigid limit to the speed of evolution. If we give up the assumption of independent fitness, evolution can go at any speed we like. Selection by means of differential fertility may also offer a way out of the Dilemma, though I have argued above that it is not a panacea.
It remains a matter for empirical research whether rapid multi-locus selection is a common evolutionary phenomenon, and if so what is the selective mechanism that permits it. This also has implications for other problems in evolutionary biology. For example, some theories of the advantages of sexual reproduction (e.g. Kondrashov's) require patterns of synergistic fitness effects of a kind that might also solve Haldane's Dilemma. The Dilemma also seems relevant to the theory of punctuated equilibrium, where it is claimed that most evolutionary change occurs in relatively short bursts in between long periods of stasis. Yet Haldane's 1957 paper is not mentioned in S. J. Gould's vast book on The Structure of Evolutionary Theory. Maybe the time is right for some joined-up thinking?
Note 1: some commentators have misinterpreted Haldane as arguing that only one gene can be under selection at a time, at intervals of 300 generations! (see for example this Wikipedia entry). This is complete nonsense, and a travesty of Haldane's paper.
Note 2: not all biologists dismissed the problem. For example, John Maynard Smith, in his 1978 book The Evolution of Sex, gave it serious attention.
Note 3: on page 520 there is a formula which may be written as n = 30 Sd, where n is the number of generations required for a gene substitution (my K), S is a summation sign (Haldane's large sigma), and d is the average fitness effect of each gene under selection (Haldane's small delta). I think this formula must be a misprint for n = 30/Sd. The formula as printed makes no sense, as it implies that substitution takes longer when selection is more intense! The correction n = 30/Sd is consistent with the rest of Haldane's working, and also with the exposition by John Maynard Smith, who gives a formula equivalent to Sd = 30/n.
Note 4: the assumption is not explicit in the 1957 paper, but it seems to be required for Haldane's calculations, and in a paper of 1960, describing his 1957 conclusions, Haldane referred explicitly to 'a population of constant size'. This requirement can be satisfied if we assume that there is always a surplus of offspring sufficient to cover 'selective' mortality, with the surplus being reduced by random mortality to a constant carrying capacity. Some commentators have seen the assumption of constant population size as an inconsistency or major flaw in Haldane's analysis, but R. Flake and V. Grant showed in 1974 that Haldane's main conclusions still hold good for varying population size and varying intensity of selection.
Note 5: If selection on each allele is strong, overlap of selection for different alleles may become significant, and reduce the overall number of selective deaths required. To take an extreme example, if all individuals who lack any of the rare advantageous alleles die, then the only survivors will be those who bear all of those alleles, and in a single generation they will all be fixed, at a cost of slightly less than 1 times the population size. The snag is that there probably will not be any individuals with all those alleles, so the species will go extinct! To take a less extreme example, if there are two rare advantageous alleles, A and B, each with a 50% selective advantage, then in each generation 50% of non-As and 50% of non-Bs will be killed, but around 25% of the population will be 'killed' by both factors of selection, so the total selective mortality will be around 75%, not 100%. Even if all the s's are individually small, overlap will become significant if there are enough alleles under selection, but this will not occur unless the sum of the s's is relatively large, which again implies likely extinction.
J. B. S. Haldane: The cost of natural selection, Journal of Genetics, 55, 1957, 511-24.
J. Maynard Smith: 'Haldane's Dilemma' and the rate of evolution, Nature, 219, 1968, 1114-6.
P. O.Donald: 'Haldane's Dilemma' and the rate of natural selection, Nature, 221, 1969, 815-6.
B. Wallace: Genetic Load, 1970.
Saturday, April 22, 2006
In December I posted a hypothesis about skin color evolution in East Asians and Europeans in light of new research which suggested that Europeans were fixed for a particular locus which explained a great deal of the variation between themselves and Africans. The facts are like so:
1) There are probably around 5 loci of major effect that explain skin color variation in human beings (older pedigree analysis as well as new genomic data seems to be focusing on a number in this range).
2) One of the major loci, MC1R, is highly polymorphic in Europeans, constrained in dark-skinned populations to the ancestral consensus sequence (Africans, to a lesser extent in South Asians), and being driven toward fixation on a derived allele in East Asians.
3) A new locus in Europeans seems fixed and is responsible for the skin color depigmentation, but in both East Asians and Africans this locus is in an ancestral condition.
From these data I hypothesized that East Asians and Europeans were genetically isolated so they reached the same fitness optimums (assuming light skin has selective benefits at high latitudes) via different genetic architectures. In Europeans MC1R is diversified (either through frequency dependent selection or relaxation) because SLC24A5 handles the phenotype. In East Asians SLC24A5 is in an ancestral state, so MC1R has been coopted via the derived allele to generate the same end via different means.
I think I was wrong, and the evil Finns are to blame...they exhibit a rather high frequency of the MC1R allele which confers light skin in East Asians, but they're in Europe! The idea that I threw out there is really contingent on powerful genetic barriers, beneficial alleles have a way of sweeping everywhere that they confer fitness all things being equal. Lactose tolerance is spread throughout Eurasia, and not because of massive population movements, while various malarial resistance alleles are pretty common across regions just where malaria is endemic. Perhaps there was a massive ice sheet in the middle of Eurasia, and Finns are the byproduct of an admixture event, but my understanding is that MC1R has been under positive selection for around ~10,000 years in East Asians. That's pretty recent, and I don't think that the genetic barriers across Eurasia were that strong for that period, they should been able to "borrow" SLC24A5 instead of throwing up their own trick de novo. Other shit is going down...and I'm sure that pleiotropy has its dirty hand involved here.
But I was wrong, though I did give it a good college try :)
Recently I've been saying that it is important to distinguish between what people believe, what they say they believe and what they do. The three do not always integrate well together. One can posit many reasons for this, though I believe some form of cognitive modularity and various social psychological pressures can probably account for much of it. It seems a trivial and obvious point, but in discussions about human motives and predictions about their behavior these issues tend to be ignored. The problem is that people have a hard time treating other human beings as natural objects. There's a reason for this, we're damn complicated and hard to figure out. Additionally, our intuitive psychology gives us a lot of "free information" concealed within our heads which we take for granted, we don't have to make recourse to explicit models because we know much of what needs to be known implicitly. We trust introspection because it works well in day to day interactions, we come preloaded with a lot of people interpretation software.
I bring this up because I was remembering a stupid thing I used to say about religious people: if the religious believe in an afterlife why do they get so scared when people are about to kill them? This was a dumb "gotcha" for showing that religious people weren't really that religious, that they didn't really believe that there was an afterlife because they didn't behave as if there was an afterlife when this life was going to get snuffed out. I've seen this come up on the message boards here too, I'm not the only person who has naively expressed this truth as if it's clever.
The problem is that we assume that people are cognitively integrated, and that there is a tight fidelity between their various beliefs and how they inform one's actions. And, reflectively, if one accepts that evolution has shaped our behavorial suite to some extent, reflexive fear of getting killed would seem to be one of the most adaptive handy mental biases! I was always a big fan of evolutionary psychology, but I was too much a moron to consider this. That is, even if someone sincerely believed that there was a life after, their "instinct" for fear would simply overwhelm their reflective beliefs in the "heat of the moment." Obviously if you didn't have this "flight or fear" sort of instinct, not matter your prior beliefs about the afterlife (most peoples seem to have some expectation of post-mortem sentience, though it usually isn't as cheery as modern religions make it out to be), your long term fitness will decrease. Ultimately you could probably think it through and come to the conclusion that it is best to run and hide, but by that time you might be dead.
Addendum: You can invert this with the "there are no atheists in a foxhole" saying, just because someone makes recourse to divine aid in a moment of duress doesn't mean they rationally believe said being exists. Many unbelievers I know have a strong bias toward wishing there was a divine being, they simply can't reflectively convince themselves that its existence is plausible. It makes sense that native cognitive biases can shunt aside reflection in situations where cost of philosophical inconsistency seems trivial. This sort of in-the-moment apostacy is well known in in religious circles, the Donatist movement in ancient Rome arose because so many Christians, including bishops and church leaders, had apostasized under threat of persecution and death. The orthodox position was that apostates had to be forgiven because of considerations of human nature, while the Donatists rejected such compromises. The reality is that the apostates were almost certainly sincere Christians, they often reverted back the first chance they got, but they also had a strong instinctive fear of death, so they compromised their principles.
Friday, April 21, 2006
When trying to get across the gist of complex technical subjects to a layperson, sometimes a good metaphor can do more pound-for-pound explanatory work than hurling large amounts of jargon-laden details.
Fore example, Gary Marcus provides a lucid explanation of gene expression by analogizing each gene to a conditional statement in a software program. Each gene has a set of conditions under which it's expressed (IF/WHILE), and a specific protein it generates when activated (THEN/DO). While this is most readily intelligible to people with experience in computer progamming, it can be understood by intelligent non-programmers with a little coaxing and can clear up several confusions and help order one's thoughts:
And so forth. Another good example for the numerate is the definition of race that got Steve Hsu's comments deleted by Brad DeLong: represent each individual's genome as a point in a space of extremely high dimension, and define a race as a set of points whose distance from each other is less than some radius. These clusters map onto intuitive self-identified race with a very high degree of accuracy.
A third example (which I first encountered from Henry Harpending [PDF]) is analogizing intelligence to size. Many opponents of IQ testing start from the correct point that there is no single definition, measurement or task that completely captures everything we consider "intelligence," but then slide from there into saying that IQ is meaningless and intelligence can't be measured.
If you substitute "size" for "intelligence" it becomes apparent just how silly the argument is. Height is one dimension of a person's size, as is shoulder breadth, weight, the length and circumference of one's limbs and so forth. There are short guys who are built like tanks and tall guys who'd blow away in a strong wind, but nobody takes exception to the concept of "size" on their account or argues that size can't be measured.
This cuts both ways: it also suggests that attempting to reify g is a category mistake. Like the concept of a center of gravity, g is an abstractum, a theorist's fiction -- but one that is well-behaved and has a causal "reality" to it all the same. We can predict that someone with a high g will perform well on all kinds of cognitively challenging tasks just as we can predict that a chair tipped on its back legs past a certain angle will fall over.
Since GNXPers are used to dealing in complex subjects which are very misunderstood and commonly regarded with perplexity (if not suspicion or outright hostility) by laymen, I thought it might be worthwhile to solicit whatever other metaphors y'all have found useful in both understanding and explaining technical concepts. They don't have to be biology-related, though I expect most will be. Discuss amongst yourselves.
Update: John Wilkins responds thoughtfully to the brief treatment of race here, but I think he and PZ Myers, both professed Lewontinites, ultimately miss the boat. John gives it away thusly: "So, do I think there are races in biology as well as culture? No."
Asking whether race exists in this way is a category mistake, albeit an all too common one. Race is another abstractum, like the general intelligence factor. How we define it will be wholly a matter of convention, though not totally arbitrary because some definitions obviously have more utility than others. Returning to the initial representation I used, you could shrink the race-radius right down to the point where each individual (plus his twin, if he had one) was his own distinct "race" if you wanted to, but this wouldn't be interesting. If all that one means by "race is a social construct" is that one can can twiddle the granularity of racial categories virtually however one likes, then this is perfectly true and perfectly beside the point.
Because at bottom, all this abstraction and definition is based on a real molecular substrate. Piles of rock and dirt don't change their height based on whether one choses to call them hills or mountains. Hypertension doesn't suddenly stop being more frequent in African men based on how one decides to classify them. Genetic variation between populations doesn't become any less real. Eppur si muove.
Update the 2nd: GMTA. Razib goes on at greater length and depth, as usual.
I made a recent post on male-female drowning disparities in maritime accidents. As the subject generated a whooping 51 comments, let's follow up that blogging success with a new study on the black-white Drowning Gap:
The findings, published in the American Journal of Public Health, not only confirm past research showing that a large number of young drowning victims are African American, but also identify where these deaths are happening.
"5 to 12 times higher?" Hmm...
Fun fact of the day: The built-in Blogger spell checking software does not recognize the word "blogging". Heh.
A week ago I was in a hiphop dance workshop, and the weekend submersion in hiphop culture reminded me of this OSR post on the globalization of hiphop. Today this seems pretty relelvent, witness this lgf posting.
But the global appeal of hiphop is not exclusive to Palestinian youth--hiphop culture appeals to marginalized youth everywhere.
Where hiphop culture enters a society, it tends to become the youth culture of the society. I'm a J-horror otaku-- in the opening frames of Ju-Rei (the uncanny!) we see a quadrette of japanese schoolgirls street dancing in front of a darkened Tokyo storefront window (right before the Dark-Shadowed-Girl eats them up). In chapter nine of Global Noise, Ian Condry surveys the japanese hip-hop scene. In Japan, street dance first introduced hiphop culture to japanese youth. There is not a single mention of crack in any japanese lyric-- instead J-hiphop focuses on the commerciality of japanese society and the tension between club scene hiphop culture (heaven) and school/work culture (hell). Dance introduced hiphop culture to Korea as well. In Korea, becoming a "dancing hero" is a dream of escape from poverty for young Korean men.
What I find most exciting about the globalization of hiphop, is the idea of an emerging popular global culture, cross-fertilization and the idea of "flow", that the boundaries of nation, culture, race, and language are becoming permeable. A medium of expression for youth culture that doesn't feature broken shop windows and burning cars. I'd rather have disaffected arab youth become rappers than suicide bombers anyday.
And the idea that any marginalized youth culture group can express themselves through hiphop is wonderfully hopeful to me. For example, fundamentalist christian youth in America could be considered a marginalized group among their peers. They advocate abstenance and modest dress and virginity. Yet even the fundies can exploit this medium. The title of this post comes from one of my favorite hiphop albums-- Holy Culture by the Cross Movement. I've made two dances on the songs so far--their flavor is hot!! This is from Rise Up. And yes, emminently danceable.
We're goin' live this life
Stay tuned for the next installment-- Islamic Hiphop versus Islamophobia: Hiphop Culture in MENA
Thursday, April 20, 2006
I suppose I shouldn't be too surprised to read that the blogger who runs Pandagon has come out against surrogacy which, in effect, means she's against gay men being able to have children together because in doing so they would have to involve a woman's uterus and her argument is that "Surrogacy is the wet dream of the patriarchy" which leads her to conclude that "I'm opposed to surrogacy outright."
It's very interesting to watch the ideological inconsistencies of feminist principles batter against each other. It's no surprise to me that I'm a stronger supporter of reproductive rights than feminists who obsessively filter the issue in terms of how it relates to "THE PATRIARCHY." It should be interesting to watch their responses to the growing mindshare of Pre-implantation Genetic Diagnosis and the choices that will present with the onset of genetic modification technologies.
This is what happens when you keep your eye fixed unwaveringly on what "THE PATRIARCHY" is up to, you kind of forget about other groups' interests. I just can't see how gay men will have children without the use of a surrogate, that is, not until we develop the artificial uterus, which of course will open up a whole can of worms for feminists - should they support the right to fetal extraction or fetal extinction. If they can't point a finger at "THE PATRIARCHY" where, of where, will they ever find the principles to guide their feminist dialogue?
Related: Anti-Liberal Bias, PC suppresses speech, ideas and now genetic choice.
UPDATE: Ilkka Kokkarinen takes on the Leftist objections to outsourcing surrogacy.
Check out this cool paper in PLOS Genetics:
I hope John Hawks and the gang can get their buddies to lend them some ancient DNA! The character of human evolutionary bottlenecks is a major issue in how we view the origin of our own species. There is other cool stuff about founder effect speciation (founder flush?) and the evolution of sociality via kin selection. Oh, and I don't know where the molecular clock variation across taxa debate is now, but I'm still a little surprised that after 2,000 years a rodent species couldn't "bounce back" a little more mutationally.
Now, we know that Europeans seem to be light in skin color because of fixation of a derived allele at a locus other than MC1R. In contrast, East Asians are "ancestral" at the locus where Europeans are "derived," but they show evidence of strong positive selection for the Arg67Gln haplotype on MC1R. Here are Arg67Gln frequencies by population (source):
Papua New Guinea 12.5%
UK Asian Indians 4.5%
Southern India 2.3%
Ivory Coast 0.0%
The Gambia 0.0%
UK Africans 0.0%
Along with data from TAT C it makes you wonder. They used to say you scratch a Russian and you find a Tatar, well, if you scratch a Finn....
A novel domain suggests a ciliary function for ASPM, a brain size determining gene:
In the GNXP Forum I have placed a PDF titled skincolorsexual.pdf. It is the full PDF of Sexual Selection as a cause of human skin color variation:
Since I've put the full paper online, I suggest people actually read it before they comment (*hint*).
Wednesday, April 19, 2006
Since nobody else has noted it on here yet I figured I might as well: Griffe's poked his head back up for the first time since the Summers flap, with an essay on "Politics, Prison and Race". Nothing particularly new here -- using similar methods as he's used in past essays, he posits a model to explain the ironic fact that black/white incarceration ratios in the US correlate positively with the "progressiveness" of states and their governments.
The short answer is the same as with sex differences in the mathematical sciences -- due to the difference at the tails of the distributions, the higher you set the threshold the greater the disparity will be. More "progressive" states tend to set higher thresholds for incarceration, ergo the higher B/W imprisonment ratio. It's straightforward, and given the crudeness of the model it fits the data passably well.
I know I'm not the only poster here who finds this sort of "ideal gas model" approach remarkably frustrating in its limitations. Suggestive though it may be, one could sit and poke holes in it all day, and ultimately the macro model persuades nobody until you've given it microfoundations...
Next Tuesday Kuala Lumpur will host an important two day seminar on Islam and Life in Space. With Malyasian astronauts likely to be sent to the ISS by the Russians there is an urgency to the question of how Islam should be practiced in the unique conditions of space. For instance, with the station orbiting the Earth 16 times in 24 hours can the astronauts do any work on the station when they are praying 5 times every 90 minutes? Also, will they have to change the direction they pray in as the position of the ISS changes in relation to Mecca as the ISS progresses on its orbit? Vexing questions indeed.
I'm not an alien. With that declaration out of the way let me say that I'm starting to think that perhaps I'm not part of the demographic that CBS is targeting for their show NCIS. I have deduced though that the demographic that is targeted must have something to do with aliens, either as the audience or as the subject matter for the series. Here's where my reasoning has taken me so far:
1.) This unit is a deep undercover gov't agency that is simply masquerading as a Naval Criminal Investigative Service unit. It's primary mission must be investigating the mysterious deaths of the aliens in our midst who have assumed cover identities as naval personnel. This conjecture is supported by the scenes which take place in the autospy room where the victims of foul play are completely devoid of nipples and genitals as they lie naked on the coroner's examination table with their chest cavities cut wide open and their skins peeled back. Clearly, the series pulls no punches in showing the graphic details of autopsies so the absense of human sex organs and nipples must be a major clue that the series is really about the sexless alien victims of crime.
2.) The targeted demographic may be the aliens amongst us who do not realize that humans actually have sex organs. The graphic depiction of a skull half blown away from a bullet exit wound should be a little more troubling to people than showing a woman's nipples as she lies on the exam table. One would think that if humans were the targeted demographic for this series that CBS wouldn't be celebrating the variety of ways of butchering humans and shying away from the accurate depiction of the human form.
3.) It is possible that the autopsy unit of NCIS uses alien technology in their examination lighting, where the light beam possesses the ability to make items invisible as the brightness of the light beam is increased.
I just can't decide which alien angle CBS is playing out here. Can you?
Tara at Aetiology has a post about pictures of hot chicks making masculine guys less prone to be hard-asses. This might fall into the "and someone funded this research???" category. Nevertheless, I have two stories to recount about "hot" chicks which readers might find amusing.
First, a few years ago a friend of mine was in the passenger seat of a van that was passing by one of the bridges that cross the Willamette from the east to the west side of Portland. He noted that a young joggeress was making her way to the bridge, and watched as a man in a truck rubbernecked to the point where he didn't notice that there was a car in front of him in the intersection. His truck and the car in the intersection he should have stopped for crashed perpendicularly into each other. My friend saw the whole thing go down, and he leaned over to the driver's side and said to his friend, "That chick just caused a crash!" His friend was like, "Yeah, she could, couldn't she?" Turns out he was rubbernecking the whole time and didn't even notice the crash! I asked if the chick was hot, and my friend was like, "It's Portland, of course not."
Another story concerns myself. I was on the road with a friend and we were in a town with very few attractive chicks. Then, across the street I spied someone of considerable pulchritude, so as I walked on my side of the street my eyes were tracking her...and I ran into a tree!
Tuesday, April 18, 2006
I was skimming through Glenn Conroy's Reconstructing Human Origins today, and it was like I was reading John Hawks' weblog. Conroy spends a good chapter ripping into simplistic conflations of gene genealogies with the evolutionary history of a species. He hits points like the likely non-neutrality of mtDNA & Y lineages, the affect that different population sizes have on phylogeographic reconstructions and the loci which fly in the face of a simple out of Africa model. Here he is in plain English:
Like I say, morphology does not imply phylogeny. Unfortunately, the mixed "mostly Africa" model that Conroy seems to lean toward escapes pithy sloganeering and summation in the manner that Out-of-Africa and Multiregionalism seem amenable too. Out-of-Africa's one shot expansion from a fixed space and time to fill up the world is pretty easy to conceive of. Similarly, Multiregionalism as old fashioned anagenesis could be conceived of as a flux of genes amongst a node of fixed populations. The reality might very well be a palimpsest of nodes overlain with important demographic expansions from particular locales, along with the important caveat that regionally adaptive genes might flourish indefinitely while ancestrally informative alleles sink or swim in the soup of migration, mutation and drift. Oh, and while I'm at it, "Nature vs. Nurture" is an idiotic dichotomy.
Monday, April 17, 2006
Liza Gross has an essay in PLoS Biology, "Scientific Illiteracy and the Partisan Takeover of Biology", about Jon D. Miller's work on scientific literacy.
The good news:
Only 17% of adults in the U.S. are "scientifically literate," but that's higher than in Canada, Japan, and Europe.
The bad news:
in a 2005 survey measuring the proportion of adults who accept evolution in 34 European countries and Japan, the United States ranked 33rd, just above Turkey. No other country has so many people who are absolutely committed to rejecting the concept of evolution, Miller says. "We are truly out on a limb by ourselves."
Miller sees opportunities for learning everywhere and may be one of the few people in the scientific community to see an upside to Big Pharma's ubiquitous direct-to-consumer TV drug ads. By saying that cholesterol levels derive from two sources-diet and family history-commercials for Lipitor and other cholesterol-reducing statins introduce the notion that genetics is probabilistic rather than deterministic in a very basic way that people can understand, he explains. "But if you say that genetic predisposition is 'probabilistic,' you've just lost 90% of the people."
Via Dienekes, Study explores how accurately men gauge paternity. The paper itself, How well does paternity confidence match actual paternity? Evidence from worldwide nonpaternity rates, has been available in preprint form for a while now. I mention it here in part because it can sometimes be difficult to track down the reference in our archives. The paper seems to point to the reality that type I error (false positive) seems common when it comes to suspicion of paternity, but honestly, 1-2% rates of type II error isn't all that reassuring to many men I suspect. As the post-genomic era advances it seems plausible that routine screens of families for genetic predispositions are going to put professionals in sticky ethical situations, though I assume they would keep any pattern of glaring genomic discordances to themselves....
Sunday, April 16, 2006
You want evidence that Finnish people are freaks? Watch this video (very not work safe).
Hat tip, Josh, Evil-Baby-Photographer.
P.S. Jaakkeli && GNXP = top two hits on google for "Jaakkeli."
P.P.S. Is this Jaakkeli???
From Nature, Independent evolution of bitter-taste sensitivity in humans and chimpanzees:
Related: PTC taste, balancing selection?, PTC, part II, Taste & behavior genetics, Genetics of taste and Slow & diverse food.
No shot will go unanswered! Anyway, here is a response from Judith Rich Harris to Agnostic's review of No Two Alike:
Saturday, April 15, 2006
Last fall when I read a spate of books on Catholicism in the United States I noted that many scholars perceive 1960 to be the "high point" of organized American Roman Catholicism. John Kennedy was elected, and Roman Catholics were no longer viewed as the papist "Other," but neither were they embroiled in the culture wars. How things change....
As some of you know, Asian Americans, specifically Filipinos and Vietnamese, make up 12% of seminary students. But what about Hispanics? 15% of seminarians are Hispanic. Assume that 25% of America's Asian Americans are Catholic (less than 50% are Christian), they are around 4% of the population. Hispanics are 60% Roman Catholic and around 12% of the population. These numbers imply that Hispanics are around 25% of American's Catholics, while Asians are 4%. From One Nation Under God (1994), page 139:
In the past the Roman Catholic Church in the United States was pretty resistant to any demand to make priests somewhat representative of the parish. Italian parishioners resentful of their Irish priests seems to be part of ethnic American lore. We'll see if the modern Catholic Church has the will to resist the cultural zeitgeist of proportionalism.
As some of you may know I quite enjoy going to blogs in which my comments are classed as contrarion. Unfortunately, like the fervent Marxists of old, today's zealous defenders of the faith are just as intolerant of having dissenting opinions appear in their midst. Here's how the feminist version of a Communist show trail takes place:
First a commenter by the name of Radfem makes a reference to the Black Version of "The Protocols of Elder" which contains reasoning like the following:
A few commenters and I chime in to point out that bringing this kind of reasoning into a discussion is like quoting "The Protocols" and then the blogowner chimes in:
Shortly thereafter Charles makes his appearance in comments. His mission is to play the role of a modern day Savonarola, or in this case, the prosecutor who presents the case of my ideological heresy. He claims the following:
He's objecting to my comments which disagree with his vision of a racist white populace trembling in fear of the demographic change that is occurring in our nation. To make my point even clearer I respond:
This provides Charles with all the ammunition he requires for his devastating hammerblow which he provides in the summation of, what to me was at the time an unknown prosecution:
Did you catch the ever so subtle tactic of arguing against the strawman? I know it's subtle and you really have to look for it, but apparently when the judge is a tool, or a fool, it can be very convincing:
Note the reaction of this innocent bystander, who apparently, has not been getting drunk on the kool-aid:
Hang around in the femisphere long enough and this type of crockery passes for regular reasoning. The surprising aspect to all of this is that the Christian fundamentalists and creationists that the feminists mock so severely are actually more tolerant of dissenters in their midst, at least from my own experiences, for I've never been banned on their sites as I, an athiest, argue about the existence of god, and the follies of intelligent design and creationism.
Now, moving beyond this little, completely inconsequential, squall in the blogosphere, the same dynamic of invading the insular little worlds of ideologues is also occurring in the universities of the world. Today, the Sydney Morning Herald publishes an editorial on the Andrew Fraser Affair:
Related: Climate of Fear in Academia.
Friday, April 14, 2006
Over at my other blog I offer opinions as to the reality that physicists are more intelligent than biologists when it comes to g (I wouldn't be surprised if theoretical physicists weren't the best when it comes to eye-hand coordination, but I won't hold that against them). My rough conclusion is that if you had a math olympics between the average physicists and biologists obviously the physicists would wipe the floor with the latter, but, since the raw number of biologists is so large if you had to assemble an "all star team" the biologists might be able to compete because the sample space of possibilities is so much larger.
But that's not what this post is about. I barely skimmed the other test score averages from ETS, but I did note that the highest verbal and analytical writing scores were from people intending to major in philosophy. I found that kind of interesting.
Thursday, April 13, 2006
Almost ten years ago, Judith Rich Harris (The Nurture Assumption) reviewed the literature on the tiny role played by the "shared environment" -- i.e., anything two people growing up in the same household share -- in shaping adult personality and intelligence, a central finding of behavior genetics. Depending on the particular trait measured, roughly 40 - 50% of the variance in personality and intelligence among individuals in a population is accounted for by genetic variation; typically 0 - 5% is accounted for by the shared environment; while the rest is lumped into the category "nonshared environment." It is this latter category to which Harris now turns her attention in No Two Alike. That is, what causes identical twins reared together to turn out any other way than exactly identical?
II. Micro noise
Rather than lay all her cards on the table at the start, she crafts the book to read like a detective novel in which suspects are eliminated one by one, only to reveal her original thesis near the end. However, I'll take a more conventional approach in reviewing her work by getting straight to the punchline, stipulating that none of the usual suspects (birth order, etc.) is the real culprit -- except for "developmental noise" (DN). Her phrasing of DN (p. 46):
There are biological differences between identical twins, due to unpredictable things that happen before and after they are born. A neuron zigs instead of zags. One fetus occupies a better position in the uterus. One twin falls down the stairs or contracts a virus. Exposure to pathogens has been proposed as a possible etiological trigger both for schizophrenia and for type 1 diabetes. The schizophrenic twin may have developed the disorder not because her life was more stressful but because she happened to encounter a virus at the wrong time.I'm going to belabor this point, looking only at infection, since Harris did not elaborate on it, as she was concerned with social causes of personality differences. In fact, the boldfaced phrase above could be amended to say that "both twins contract a virus, but in one, and not the other, it travels to the nervous system." Sound crazy? This is just what happens with polio (pdf), which typically resides in the gastrointestinal tract, but occasionally gets into the nervous system:
Up to 95% of all polio infections are inapparent or asymptomatic. Estimates of the ratio of inapparent to paralytic illness vary from 50:1 to 1,000:1 (usually 200:1). . . Fewer than 1% of all polio infections result in flaccid paralysis.And consider the MZ and DZ concordance rates (in %) for the following known infectious diseases, where presumably both twins were infected (Vogel & Motulsky, Human Genetics, p. 237; search the Amazon page for "tuberculosis" and flip to that page):
Measles - MZ = 97, DZ = 94If MZ twins are barely more concordant than not for tuberculosis, and more discordant than concordant for pneumonia, the chain from infection to symptoms must incorporate a fair amount of chance. In principle, the same thing could play a role in individual differences in personality. I earlier wrote (here, here, and here) about why we should expect something like this. Briefly, the very existence of the brain-blood barrier (BBB; kiddy link with more sophisticated links therein) suggests a timeless struggle to keep microorganisms out of our control center. Because microbes evolve (and quickly), we shouldn't expect the defense to hold up forever, nor against all invaders. Aside from known infectious diseases of the brain such as bacterial meningitis (which uses a Trojan Horse ruse to cross the BBB), the mere fact that we can chemically affect mood and personality using drugs such as Prozac demonstrates how easily microbes could invade the human central nervous system and alter mood / personality.
This is all the more likely in regions of the brain without a BBB, such as the hypothalamus, which in turn is part of the limbic system, thought to be the emotional center. Moreover, the BBB is not fully formed even in toddlerhood. In any case, this is where you would want to head if you were a virus that had long-term (rather than acute) plans for your host -- commandeering the visual or auditory systems wouldn't do much for you (if anything, it'd make the host blind or deaf); ditto for the seats of higher reasoning. If the human brain is like an airplane that you, the long-term-minded virus, are hijacking, you want to keep pretty much everything in working order -- except the part that deals with setting the destination, which is like the motivational and personality components of the brain that set goals and steer toward them. All a virus would have to do is supply a different set of coordinates to the pilot; everything else would take care of itself.
As an aside, some viruses might not even be keen on hijacking the brain -- some might merely be interested in a preemptive strike against the brain's most sensitive pathogen-detectors: our "chemosensory" senses of taste and smell (we can't hear, see, or feel microbes). It so happens that parts of the limbic system (such as the amygdala and hypothalamus) also deal with these less conscious aspects of taste and smell (e.g., how palatable something is, as opposed to discriminating two brands of soda if you were blind-folded). So, a virus which attempted to knock out our pathogen-detectors might cause minor collateral damage that subtly altered personality.
The notion that a tweak so subtle could turn one from an introvert to an extrovert may sound exotic, but in a 2002 review (pdf) of animal models of infectious obesity, the authors emphasize:
Noteworthy in our experiments was the absence of gross histological changes in the brain of many obese animals; had the fact of an initial virus infection not been known, there would be no virological or histological evidence that the observed obesity syndrome had its origin in a preceding viral infection.In other words, an infection both fleeting and nearly impossible to detect (unless you already knew what to look for) had a large effect in turning infected animals obese. By the way, the part of the brain infected in their studies was the hypothalamus. In sum, I see no reason why something similar couldn't make one more extroverted, less conscientious, and so on.
III. Social noise
Moving on, her original thesis is that some of the nonshared environment consists of differences caused by your competing for status by examining other people's mental "profile" of you. She proposes three psychological mechanisms to account for this: the relationship system, a mind-reading device, and a status system.
The first is like a mental rolodex whose purpose is to keep track of socially relevant information of individuals: their face and name by which to uniquely identify them, their relationship to you (brother, close friend, boss, spouse, etc.), and other information relevant to how well they can contribute to your survival and reproduction -- are they mean or welcoming, bright or dull, do they return favors or not, do they still owe you any favors or not, are they sexually interested in you or not, and so on. The mind-reading device is the standard theory of mind module used in many cognitive & evolutionary psychology models of how our mind is built. In essence, its purpose is to allow you to peer into the mind of another individual to facilitate social behavior -- does that narrow-eyed look she's giving you mean she's trying to threaten you or seduce you? (Or both, perhaps, if it's role-play.) What did she mean when she put a funny intonation on "I'll" as in "All right then, I'll do the dishes"? And so forth. Last, the status system pushes you to attain high status within your peer group, which is mostly based on physical dominance in young males and good looks in young females. Since in pre-modern times higher status (so defined) likely increased reproductive success monotonically, the purpose of this system is clear enough: it compels you to reach a status level where you'll have the most kids.
Now, here's how she accounts for the non-shared environment: part of personality formation comes from you adjusting your personality settings in light of what others think about you, a process that plays out really in adolescence, not infancy. That is, you use your mind-reading device to see what information is listed in your profile in someone else's relationship system. However, because you want a large sample size to base judgment on, you look into the relationship systems of everyone who has an entry for you and average the results. This composite profile is what the "Generalized Other" thinks of you, and you adjust your personality accordingly. If they regard you as a diminuitive wimp, it won't pay in the status competition to be aggressive and cocky. If they think you're a dependable leader, it pays to be more extroverted. This ties in to the non-shared environment because identical twins won't necessarily have identical composite profiles once they've read the minds of the Generalized Other -- e.g., one may owe more favors than the other, and thus may be perceived as less cooperative.
I'll quote her at length since this is the core of her thesis. Here are the three ways she believes this interaction between the three devices can produce personality differences between identical twins reared together (p. 230-1):
[W]hen [MZ twin 1] tries to read what you've recorded about him on his page in your lexicon [i.e. relationship system], he will see something different from what [MZ twin 2] sees. . . They don't get the same social feedback because your relationship system has discriminated between them. The relationship system is far more interested in the differences between people -- the things that make each one unique -- than in their similarities. (original emphasis)In other words, to the extent that MZ twins have non-identical profiles, they will respond in non-identical ways. However, recall that a person examines the average profile of themselves which they've read from the minds constituting the Genaralized Other -- not just of one other person. Therefore, this scenario could produce differences only if the average profiles were different -- and that just pushes the question back a level: what led to MZ 1 and MZ 2 having different profiles in adolescence? Since under Harris' view their genes and almost all relevant social experiences have been near identical up to this point, it must be that chance factors large or small have resulted in this discrepancy. For example, Donald's amygdala was subtly lesioned by infection but not George's, resulting in divergent composite profiles gotten from the Generalized Other. So, this is due to developmental noise (DN).
Within a group of boys, only one can be the toughest. Within a group of girls, only one can be the prettiest. If a group contains a pair of identical twins -- even if they're both very tough or very pretty -- one will inevitably be second best and the other will rank higher in the attention structure. The twin who receives more gazes [i.e., the one the others pay more attention to] will tend to speak out more in the group and will consequently receive yet more gazes, so that what might have started out as a tiny difference will widen.This differential attention-getting could be due to pre-existing differences -- which in this scenario cannot be due to their shared genes or shared environment, and thus would be due to DN -- or when they're together, by chance MZ 1 gets 49 of 100 gazes, while MZ 2 gets 51 of 100, which then snowballs via a postive feedback loop in favor of MZ 2. So again, this is just DN.
Last, social cues you use to read the minds of the Genaralized Other may be ambiguous:
[S]ocial cues that you repeatedly receive from others in your group may be based on things that shouldn't have any evolutionary significance at all, because they're random. You tripped and fell at a dinner party and landed in the salmon mousse. . . You made an offhand remark that was interpreted as a prediction and the prediction happened to come true. Incidents like these can give an individual a reputation that can persist for years, spread and perpetuated through gossip.Harris admits that some random events don't have lasting consequences, but others do: e.g., "a random event can cause everyone in your group to think you're wise or clumsy or funny or brave, and to go on thinking that for years." The Generalized Other, in her view, may be responding in a predictable, non-random fashion -- thinking you're clumsy when you tripped into the mousse -- but the initial event was due to chance, like choosing the seed of a random number generator, which then obeys a rule-governed algorithm for arriving at the result. Once more, we come back to DN.
To sum up: all three reasons Harris gives for why the interaction between the three devices can account for personality differences in MZ twins are actually variations on DN. Her earlier treatment of DN was based on chance phenomena at the "micro" level of axons and hormones, but her proposal is just a "macro" or social version of the same. This is not a criticism, for although I don't think Harris' proposal is what she says it is (i.e., an alternative to DN), it specifies the mental mechanisms for how DN can occur systematically at the social level in personality formation, a novel contribution to personality psychology.
I did not know who Nicholas Steno was until today. Did you?
My ideas here. I want to put the engineering in "social engineering."
Wednesday, April 12, 2006
Below the fold is a list of books with 1 or more purchases in the first 3 months of this year via the Amazon Associate system I set up on this weblog.
In a recent post, Steve Sailer quoted an unnamed feminist as explaining the high proportion of women surviving the Titanic disaster with:
women having more body fat. Better to float and survive in the cold with.
To establish if there is any truth to this thesis, it can be interesting to compare the Titanic to other sea disasters where circumstances made chivalry a non-factor. One such disaster is the loss of the M / S Estonia, which took place in the Baltic sea, on the 28:th of September 1994.
The Estonia was en route from Tallinn in Estonia to Stockholm in Sweden in rough weather with 989 passengers and crew. Sometime after midnight, she capsized and sank rapidly. A mayday went out at 00:22. When rescuers arrived nearly an hour later, the only signs of life were the lights from the life rafts in the water. Only 137 people survived. Many perished in the cold water waiting to be rescued, but most did not make it out of the ship.
The rapid chain of events in the case of the Estonia made chivalry moot; it was by all accounts 'every man for himself', as organized evacuation efforts broke down relatively early, when the increasing list of the ship made it ever more difficult to get out.
This gives us two situations for purposes of comparison, one with Chivalry (I.e. organized rescue following the principle of 'women and children first') and one without. Below are the facts at hand:
In short, while the proportion of women rescued was almost four times as high as the proportion of men saved on the Titanic, on the Estonia the same statistic shrinks to 0.2.This is hardly conclusive, given that one can argue about specifics, but rather illuminating nonetheless.
For those of you interested in the disaster, here is the Wikipedia page. The number of conspiracy theories surrounding it certainly rivals 9/11, fuelled by an official investigation many consider lacklustre. The official disaster report was recently heavily criticized by an official Estonian government report, and there is currently an effort in the Swedish parliament to reopen the investigation. You can read more about this (if you speak Swedish) in 'R&D' which is the Swedish equivalent of 'The Hill'.
Tuesday, April 11, 2006
Since we are talking about blondes I thought I would bring to everyone's attention this thread which has an interesting collection of photos of non-black hair color about Aboriginal Australians and Melanesians. They seem to have scanned up Birdsell's map of blondism frequencies:
Now, a reasonable question to immediately ask is "is this introgression from admixture with Europeans?" I gave some reasons why this is unlikely earlier, but I think we should not rule it out in the case of Melanesians because it is well known that the peoples of the Pacific have had intercourse (so to speak) with European seamen for the past several hundred years. But, there is a reason for believing this is indigenous: the hair color is often the only "evidence" of European ancestry one can find in these individuals. Their skin is very dark, they never have light eyes and their facial features are population-typical. Granted, if you had admixture in the past and subsequent random mating you would expect that within a large enough population fragments of European traits would emerge now and then, but the key is that non-black hair is the only "European trait" in evidence. To me the most important point is that blue eyes don't ever seem to show up even though this trait is more common than blonde hair among Europeans.
So let's assume the veracity of this trait. Some of us, who have read our C.S. Coon aren't surprised by non-black hair among the indigenous peoples of the southwest Pacific, the question is, why do we see this trait only here outside of Europe? I don't know, but one pet idea I have is that during Neolithic revolution in Asia a lot of peculiar human variation was wiped out by the demographic wave of advance of Chinese rice farmers. Only in places like Papua New Guinea, Melanesia and Australia have out-of-the-norm appearances remained.
Now, another final question, why are the Aboriginals so damn dark so far south? Julian O'Dea has pointed out that Tasmania is at the latitude of Corsica, so the southern continent isn't that far south, but, Napoleon was a white man. I proposed at one point that deme-to-deme diffusion of alleles from fair skinned northern Eurasian populations couldn't move past the cordon of tropical southeast Asia, and that Australian Aboriginals did not possess the standing genetic variation from which selection could operate, but they had enough variation to exhibit a hair color range.
Update: Some of you probably want to look at this (click here for larger image)....
Genes Predict Body Shape and Fatness:
The study is supposed to over at the PNAS website as of yesterday, but as usual their webmaster is a lazy ass and hasn't put it up (I can't find it in PUBMED either). What I would like to know about are alleles which have strong life history effects, I know way too many people who had "fast metabolisms" into their twenties and just blew up because they didn't change their eating habits to track the change in their caloric burn rate.
Update: Agnostic speculates about curves (with visuals).
Monday, April 10, 2006
Aziz Poonawalla has started an sf & anime weblog. If you are the type who knows what a "Dalek" is, well, check it out.
Sunday, April 09, 2006
To google with love, from godless capitalist:
I'm a bit confused. Offhand I stumbled upon this wikipedia and IMDB entry which stated that in 2004 Vendela Kirsebom (picture after the link) revealed her biological father is ethnically Turkish (Norwegian mother, born in Sweden). I had a hard time believing this, but I tracked down this article. It's in Swedish, but English speakers can make out the gist pretty easily, and if you put it through a translator it will become somewhat more intelligible. I note that Vendela is still listed as the "archetypical" "Hallstatt Nordic" on the Angelic Beauty: a tribute to Nordic women website, but I guess it's a geocities page, can't expect constant updates. Her looks haven't changed, and of course there are many fair Turks (when I was a kid there was a giant redhead troglodyte of a Turk that would terrorize the smaller kids at the mosque every Eid al Fitr). In any case, Vendela apparently believes in heritable differences in national characters, just like Greg and Henry, she says her personality is more Turkish than her appearance. No wonder no one guessed, who the hell cares about her personality???
Addendum: In response to the stupid reader who assumed that it is more likely that Vendela's father is part non-Turkish than that he was fair...I was going to go Bayesian, but I realized the illustration of my point didn't need the added precision and formality. My assertion, loosely stated, is that the majority of people with light brown hair in the nation of Ghana are either expats or the offspring of relationships between Europeans and native Ghanians. But, the majority of people in the nation of Turkey who are fair are Turkish...they are simply a rather small minority ("fair" normalized to Scandinavian fair). Nevertheless, they dwarf the number of fair halfbloods, it isn't that halfbloods aren't fair, there just aren't many non-Turks (or Kurds) in Turkey!
I have never been to Turkey, but my mosque as a child was heavy on Turks, and though most were swarthy, a large minority did not look very "Mediterranean," and this isn't because they looked Asiatic (I was frankly shocked to learn later that Turkish was a branch of an "eastern" language superfamily via a map in my dictionary). Additionally, most of the mixed offspring of Europeans and Middle-Easterners at my mosque didn't really look very "ethnic." Half-Turks1 like David Chokachi of Baywatch fame might be a bit extreme in favoring their Nordic side (his mother is Finnish, so it is language superfamily incest), but they aren't (in my experience) totally aberrant.2
In any case, I was a little surprised to see population-normal non-distributional thinking at work on the GNXP comment boards. Most of the traffic on this site is on search engines...but I assume that the core audience can accept that their prototypes are not Platonic ideals but central tendencies? Also, I have observed a cultural bias here in that southern Europeans and Middle-Easterners who are fair are characterized as almost certainly the product of exogenous genetic input, either recently or the past, but northern Europeans like Lena Olin are implicitly assumed to be part of the normal range of variation even if they lay at one tail (in her case, coloring, her jaw is all Swedish from what I can see).
Addendum II: Just to be explicit, this is what went through my head when I saw Reale's initial comment (see the follow up, he explains himself in detail, but I don't see that he explains the previous comment).
P(A|B) = [P(B|A)XP(A)]/P(B)
In the case of P(A|B) ~ Probability of blue eyes conditional on Turkish, we have empirical data, see this map. I was being conservative in my head and assuming that 1% of Turks have blue eyes.
P(A) = foreign parentage and P(B) = blue eyes, you have probability of foreign parentage conditional on blue eyes being the product of the probability of blue eyes conditional on foreign parentage (assume European, so high) multiplied by the probability of foreign parentage (I assume very low) divided by the probability of blue eyes (evaluated within the Turkish national population). Even if you assume that only 1% of Turks have blue eyes, my understanding is that unlike Thailand or Philippines Turkey does not have a large expatriate community of whitesEuropeans who have settled and intermarried. Additionally, my understanding is that Turkey has a non-trivial indigenous blue-eyed population. In other words, I immediately inferred that the probability of Vendela's father being a blue-eyed Turk was far higher than the probability of her father being of partial foreign ancestry if he was truly a Turkish national. I could be uninformed, I guess it depends on the assumptions....
1 - In the mid-90s I watched David Chokachi tell Jay Leno that his father was from Iraq, so I assume that his father is from the Turkoman minority of northern Iraq.
2 - The variance has reasonable bounds, as I implied above. It is also a fair point that "Turks" are a genetically synthetic people who were generated via assimilation from the local substrate & enslaved peoples (Albanians & Slavs) to the Turkic elite. But that being said the ancestrally informative studies I've seen suggest only a minimal Asiatic tincture to the Turkish gene pool, and general continuity with the peoples to the north, west, east and south. Blonde Galatians and Russians are certainly part of the Turkish heritage, but the neutral marker data does, to my mind, support the contention that the fair end of the Turkish phenotype range is purely a function of admixture over the last 2,000 years with other peoples.
Friday, April 07, 2006
I mentioned on my other weblog that I have recently finished No Two Alike by Judith Rich Harris. I'll write up a review when I've thought through my impressions and reflections, but, in the meantime, one of the great things about Harris' books (The Nurture Assumption was similar) is that the wide survey of the psychological literature induces many cross-linkages and inferences that are orthogonal to the thrust of her book.
But before I get to that, let me back up and state that one of my favorite classes as an undergrad was a sociology course taught by a black graduate student. I state his race because being sociology it was a PC-soaked environment, though being a freshman chemistry major I wasn't totally aware of this initially, and he definitely used his color as leverage in making outrageous statements which seemed designed in part to goad his audience. For example, he once made an offhand comment that "there has never been a matriarchy." This elicited a rumbling of discontent from the class, and a outspoken feminist in the back of the classroom raised her hand and claimed he couldn't back up the generalization. The instructor's response was concise and precise. He laughed and asked her to name one matriarchy. She responded with something about a culture in rural Mexico (this was a collegiate legend at my university, I heard this same story about a "tribe in rural Mexico" several times over the years, but no one could recall the name of this tribe). He laughed and stated that she couldn't name it because it didn't exist.
In any case, that incident stuck with me because I'm something of an ethnology buff. Obscure peoples and their customs interest me. I've sought out books & monographs on the Yezidis, the Kafir Kalash and the Garamantes. And in all my years of searching through the literature I haven't stumbled upon a matriarchy. I emphasize the "archy" because there are many cultures that are matrilineal, matrifocal, or, where women have a prominent role in the decision making process within a society. Among the Iroquois older women had veto powers over the decisions of the male war leaders. But note that their powers were of veto, men still ultimately presented and constrained the range of choices. My overall point is that there are many cultures where men and women are rather equal in their power in comparison to the stratified societies of the Eurasian civilizations. But, the distribution is skewed, there is no inversion to the operational chattel treatment of respectable females that was characteristic in ancient Athens or modern Saudi Arabia. The alternative to patriarchy is not matriarchy, it is non-patriarchy.
Why is this? A clear point to make would be that the average male is larger and stronger than the average female because of sexual dimorphism. In fact, only 1 out of 10 males in the United States has a lower body mass than the average female. One could posit that male-female strength difference naturally results in a patriarchy on the macroscale, the idea of women treating men as chattel seems ridiculous because of their smaller size. I don't think this can be totally dismissed, and the larger size of men seems to me a barrier toward a realization of an oppressive inverse-Athenian style matriarchy in the past, but size isn't everything. I think it could be argued that the Romans who marched with Julius Caesar into Gaul and later with Agricola deep into wildest Britain were on average smaller and not as strong as the Celts they overwhelmed and cut through. Some of this is endogenous and a function of geography and the convential increase in mass as a species range expands north. Some of it was probably a function of the fact that the more "civilized" Romans might have gone further down the path of a nutritionally depleted and starch-based diet than the Celts.
In other words, size matters, but it isn't the end of the story. When you read about the counter-campaign against Boudica's rebellion, the discipline of the outnumbered Romans pays off. The behavior of the "barbarians" during this period seems likely to have been somewhat like the apocryphal tale of the Vikings on the way to Paris being asked to parley with a local noble. Their leader was asked to present themselves, at which point the Vikings got into a argument about who exactly was the leader.1
What does this have to do with No Two Alike you ask? From page 214:
[the reference is Maccoby 1995 for those curious]
I bolded the two points of interest to me. First, boys groups are larger, and second, they are more hierarchical. Is the boy the father of the man? I don't know, but he might be so. I think the rise, and dominance, of patriarchy is in part a function of the difference between male and female socialization, and the fact that male sociality scales better. The hypothesis that I am putting forward is that in the days of yore when small clusters of humans generally lived in groups of ~10-100, there was little asymmetry in the ability of bands of brothers and sisterhoods to apply group pressure on the social mores of the community. The community emerged out of native cognitive aptitudes of social intelligence that most humans possess, and that women to some extent on average possess to a finer and more generous degree than men. But as the Neolithic Revolution opened up the possibility of denser agglomerations of human society which quickly scaled up, at a certain point male dominance heirarchies were much more easily able to make themselves literally kingmakers, and the smaller female social circles simply could not compete. This is a case where the Romans were larger and more ferocious than the Gauls, not to mention more disciplined. One stick alone breaks, many tied together hold.
But, there is still a range in patriarchy, in the power of the "bands of brothers." In Marriage, a History, the author points out that in the 19th century Victorian mores that emphasized the nuclear family and romantic love between a husband and wife began to eat away at the time spent between men, especially dominant men and their underlings. Laborers during the transitionary period recounted the shift in habits as their supervisors no longer went for dinner & drinks every night, but retreated to the home. Similarly, in an inverse situation, I recall an Afghan American boy who traveled to Kabul who noted the testosterone in the air in universal male only social situations. The sexes differ, and the character of all male social situations differs from mixed-gender ones in a non-additive fashion (I can't speak to all female ones obviously).
In the past I've alluded to the possibility that "moderns" are in some ways reverting back to hunter-gatherer social mores. I think that powerful and exclusive patrilineages, the absolute exclusion of women from male social life, and the denigration of romantic love as a powerful cement in the pair-bond are characteristics that emerged after the rise of the Neolithic mass society. Of course, the trend is not universal and absolute, in republican Rome men and women ate together, in contrast to democratic Athens, while amongst the Etruscans women seem to have had a high status. There is a sample space of possibilities, but my point is that some of the possibilities are more strongly biased. The cultural world is not flat, it is textured with wrinkles, canals, peaks and valleys.
I want to tie this in to one other point that Judith brings up in her book, and that is cross-cultural differences in personality. She repeats some of the research reported in Geography of Thought and Not by Genes Alone which suggests that cross-cultural differences that we see around us can be easily shifted. For example, East Asians are more communitarian and Canadians more individualistic, but the children of East Asian immigrants in Canada tend to be individualistic as adults if they were brought before the age of 12, in between when they are brought in their mid-teens, and more East Asian if they arrive in their late teens. Geography of Thought also reports that bicultural people can quickly "switch" between mental styles. In any case, I was interested when Judith offered that Americans have become more individualistic over the last 50 years. In terms of the topic of the post, I would argue that communitarian societies on the mass scale will tend to be patriarchal, as bands of brothers will rule the roost. But, individualism, and a less structured and controlled social environment tends to tilt the field back toward women as dominance heirarchies have less power to coerce individuals toward their own ends (usually the ends of the alpha male).
Working back up to the launching point in regards to male and female groups, why the difference? There are lots of ways we could approach it, for example, males need strict dominance heirarchies because they lack the requisite social intelligence to fluidly manipulate different contexts. But, I will offer tentatively that it might have to do with reproductive skew.
Say what? OK, here goes. The Trivers-Willard Hypothesis suggests that high status females should bear male offspring to maximize their potential reproductive output because high status males can breed a lot more than high status females. There are lots of ways to rework and spin this, but that's the gist. The flip side is that low status females should invest in female offspring since these will be more of a "sure thing," as reproductive skew might result in all her sons simply not passing on their genes (because they'll never be high enough on the totem pole).
What does this have to do with dominance heirarchies? I will posit that perhaps males are phenotypically more varied that females, that is, their standard deviation on characters is greater. The idea is that the SRY induces greater developmental instability in male fetuses than female ones. Some of this is bad, ergo, more pathological or subfit males. But, some of it explores the outer edges of fitness space, and who knows when new traits might come in handy? Now, consider two women who have 10 sons. Imagine that the expectation is the same for the characteristics of sons for both women, but the variance for one woman is far greater than for the other. In a winner take all reproductive skew scenario all of the sons of the woman whose offspring exhibit no variance might not reproduce. In this case, the "risky" strategy, where a mother produces superfit and subfit sons, is the optimal one. To some extent this is a reductio ad absurdum, humans are not elephant seals, and our relatively mild sexual dimorphism is a clue that we are not a hyperpolygnous species (though we are not exclusively monogamous in the sense idealized by modern romantics).
So you have a situation where males exhibit greater phenotypic variance than females, and so establishing dominance heirarchies will be easier because more of the males will clearly never have a shot at dominance. Since the female distribution is more "bunched" together there are more potential queen bees, ergo, more competition and tumult because of a greater number of contenders. Bryan Caplan would be proud of my logic!
There's only one problem with this: I have had a hard time finding evidence for this variance difference in the past. If readers have literature citations, positive or negative (either lending support or falsifying), pass them on. I tried looking at height-weight data once, and I didn't find anything there, though at least in regards to weight Americans are not really in a "state of nature." You can find them in the psychometric data, but I'm curious about physiology and morphology as well.
1 - The near successful counter-attack under Vercingetorix during the Gallic Wars and slaughter of the Roman legions in the Teutoburg Forest under the leadership of Hermann shows that the barbarians could be devestating when organized appropriately. Note that Hermann was also known as Arminius, and had Roman training.
Thursday, April 06, 2006
The Democratic Minority Leader Harry Reid blocked an amendment which would have made illegal aliens who were convicted felons from being eligible for citizenship:
Meanwhile, across the norther border those uncouth Canadians seem to have missed the memo on how convicted felons are good prospective citizens:
Imagine holding the opinion that some people just aren't worth having as fellow citizens.
Details here (I don't use IE so I haven't read this closely).
Dienekes has an abstract of a paper out which suggests that the mtDNA lineages of some Australian Aboriginals can be traced back 40,000 years. Now remember, this is mtDNA only...looking at the mtDNA in East Anglia might suggest lighter influx of Saxons from Germany than Y chromosomal lineages. Not a big deal, but it can be hard to get details about the genetics of Australian Aboriginals sometimes.
Published today in The American Journal of Human Genetics:
Wednesday, April 05, 2006
The post that dealt with the aliens who landed on Flores has shifted toward discussing where living Neandertals (or post-Neandertals?) might reside (or what people they are). Please place your "nominations" here (I have no idea myself)....
On a related note, Anthropology.net has a post on Neandertal culture, with special reference to the Chatelperronian complex.
Also, Diana suggested to me once that Eva Green kind of has the Neandertal look going, so which side is sim, Swede or French?
Update: I misquoted Diana. I looked at the email, and she just pointed to this page (not totally work safe) and noted that some of the women, especially Julia Stiles, looked kind of "primitive." Eva Green was on that page as well.
I got local contacts Jaakkeli!
OK, not really. But, I saw in my RSS that Dienekes' weblog has a post on the religion of famous celebrities and it said Tom Hanks is "Greek Orthodox." This piqued my interest, and I found out that Tom Hanks is "Orthodox" via marriage to Rita Wilson, born Margarita Ibrahimoff, who is Greek Orthodox. Wikipedia says that her father is a Bulgarian Pomak and her mother is Greek, and I'm willing to credit this because the name Ibrahimoff strongly suggests Muslim antecedants. Pomaks you see are Slavic speaking Muslim minorities in the Balkans (as opposed to Turks, who do not speak the local language as their native tongue). Obviously Wilson was raised in her mother's religion, but according to Islam you are Muslim if your father is, and since her father was Muslim...well, let's just make sure Tom doesn't take Rita to Afghanistan anytime soon!
Related: Eliza Dushku's father is Albanian (hence the weird name).
Tuesday, April 04, 2006
Just wanted to pass the word on about Seed's science writing contest. I suspect some other GNXP bloggers and frequent commenters might be game (I can't partcipate since I'm an employee sort of).
Monday, April 03, 2006
Carl Zimmer describes a new paper from PLoS Pathogens which demonstrates a causal link between a virus and prostate cancer (full article here). Nothing will surprise readers of Paul Ewald's Plague Time, the popularized version of a journal article he co-authored with Gregory Cochran (google "infectious_causation_of_disease.pdf"). The basic logic is simple: diseases which have been around for awhile, are common, and impose fitness costs should be weeded out by natural selection if they were genetic in origin; so, such diseases are likely to be infectious. This simple point is left out of a lot of the articles on newly discovered infectious origins of common diseases (the prostate cancer article, for example), which is a shame since this theoretical guide would lead to better allocation of resources for curing diseases -- namely away from genetic studies and toward microbial studies. Indeed, a putative genetic link for prostate cancer failed to be replicated, and the PLoS article shows why: if a variant of a gene is only involved in susceptibility to infection, then a link between the defective variant and the cancer will show up only if that individual has already been infected. This point generalizes.
Also in the current issue of PLoS Pathogens is this article showing that infection of neurons with the Borna virus impairs neuronal function -- not the most basic functions, but for example long term potentiation, which is a fancy neuroscience term for the long-term strengthening of connections between neurons based on external stimuli, which is thought to underlie higher functions such as learning and memory. I'll confess that the molecular information is over my head, but for those who understand it, the authors show what molecular mechanisms are involved in the neuronal impairment caused by the Borna virus. Plague Time mentioned a link between the Borna virus and schizophrenia, mood disorders, and chronic fatigue syndrome, and only six years later we have a decent understanding of how it can cause mental disease. In fact, the PLoS authors suggest that the effects of a Borna-infected brain are similar to those observed in Alzheimer's and autism. Now, whether or not the Borna virus turns out to be the culprit for these diseases is an open question, but the implication is that this is where time and energy should be devoted if we want to cure common mental diseases.
Saturday, April 01, 2006
Justin L. Barrett is the author of Why Would Anyone Believe in God? Below are his resposes to 10 questions.
1) Most people tend to view religion as a set of rules, points of belief or a particular range of practices. Researchers who work from a cognitive prespective seem to take a broader and narrower view simultaneously. Broader in that they address the general phenomenon of religion across time and space, as opposed to specific religions, and narrower in that they interpret it through a specific disciplinary methodology. Now, people talk about religion all the time in a loose and intuitive fashion, but they tend not be systematic. Scott Atran has attempted to bring a theoretically richer and empirically grounded cognitive anthropological perspective to the analysis of suicide bombers, and it doesn't seem to have made much traction against general platitudes relating to poverty or mental insanity. Do you believe that the cognitive research program in religion will ever make an impact as an "applied social science," or will it remain at a remove from day to day public policy indefinitely?
The cognitive science of religion has the same problem in gaining traction that social psychology has had: everyone thinks that they are experts. Social psychologists have to work hard to show that their findings and insights are not just jargon-laden common sense. Similarly, most people seem to think they have a perfectly good theory of religion or religious behavior. No need to study religion! Nevertheless, as social psychology has made major applied advances (e.g., in advertising, persuasion, inter-group conflict resolution, team-building, etc.), I am confident that eventually the cognitive science of religion will gain traction. But perhaps our first applied successes will have to be in religious communities concerning religious practices and instruction and not in politically charged areas such as Islamic suicide bombers.
2) In your book "Why Would Anyone Believe in God?" you answer the question why people believe in God. More specifically, why the majority of humans believe in God or Gods. As an atheist, I have to ask, why don't I believe in God? Or, more seriously, do you believe that there are cognitive reasons why some people are just biased to be atheists? I actually emailed Robert N. McCauley about his conjecture that autistics might be 'natural' atheists because of their lack of social intelligence, but he responded that he hadn't stumbled upon any hard empirical confirmation of this hunch...yet. Do you know something we don't?
As self-proclaimed atheist Jesse Bering has observed it can be very hard to identify true atheists. He even suspects that they comprise a very tiny number of people. By true atheists, I mean people that consistently hold no belief (cognitive commitment that motivates behavior) in superhuman agency. Lots of people say they don't believe in superhuman agency (including gods and ghosts) but will still modify their behaviors around cemeteries on spooky nights ("just in case"). I also run into plenty of people who say they don't believe in God but they really have chosen to act as if they don't believe in God because they are angry with God or don't like God. With these qualifications in place, certainly there are a number of factors that might predispose individuals to become atheists. As I agree with McCauley that theory of mind or social intelligence plays a critical role in theism, those who are weaker in these areas (relative to other higher-order reasoning) might be less disposed toward theism. I find it suggestive that women-who tend to have stronger social intelligence-tend to be more religious than men; and men are disproportionately represented among self-proclaimed atheists. Autism has been referred to as a severe form of "male-brainedness," I believe by Simon Baron-Cohen. I suspect social and environmental factors are even more important in supporting atheism, and I speculate on these in my book.
3) Do you consider yourself an evolutionary psychologist?
I don't think of myself as an evolutionary psychologist even though I have a lot of sympathies and agreements with that camp. I have at least two hesitations with adopting that identification. First, I do not attempt to explain all religious or other cultural thought and behavior in terms of evolved capacities or with a stone aged perspective. The evolutionary history of a particular function of the human mind is less important to me than its contemporary properties and dynamics. If a regularly occurring cognitive structure is an evolutionary accident but still helps explain recurrent human behaviors, I'm interested. Second, "evolutionary psychology" sometimes gets identified with some controversial positions within cognitive science that I do not necessarily affirm. Evolutionary psychology often gets conflated with hard-line nativism when it comes to cognitive development; massive structural modularism when it comes to brain organization; and data-light ad-hoc theory production when it comes to theories of cultural phenomena. When trying to forge an new subfield, I suspect it is best not to identify too closely with a controversial perspective, even when it holds great promise.
4) You are a graduate of Calvin College and now work for Young Life. Do you accept the Five Points personally? If so, how do you feel about D. Jason Slone's contention in "Theological Incorrectness" that Arminianism is the natural state of the human mind?
Regarding five-point Calvinism, I'm not sure I can answer without nauseating explanation and qualifications. Within contemporary "Calvinism" we see considerable variation in exactly what the five points entail. Let me just say that I think it is completely legitimate to affirm God's sovereignty and human free will simultaneously, and I do. Slone is certainly correct that the natural state of the human mind is to assume free will of humans. Many modern Calvinists do not deny this. In fact, one of the most important 20th Century answers to the problem of pain was Alvin Plantinga's Free Will Defense - another Calvin College alumnus and former faculty member.
5) If you had to tell bicoastals one thing about Kansas which might surprise them, what would it be?
Kansas is surprisingly beautiful and I find the weather superior to that in many other places I've lived. Then there are the people. Having grown up in California but lived in New York and Virginia and spent considerable time in Maryland, I know how easy it is for bicostals (especially living in urban centers) to think that their world is normative. Academics who ought to know better seem especially prone to forget just how odd they are. Anthropologist and psychologist Larry Hirschfeld often says something about how ivory-palace academics discovering regular people are a bit like two-headed people discovering one-headed people and thinking the one-headed people are strange. Kansans are more similar to normal people-the world over-than are people from Boston or Berkeley.
6) Do you have opinions about the Intelligent Design program being forwarded by William Dembski and his confederates?
The hubbub about Intelligent Design has been a wonderful display of coalitional thinking overriding honest discussion and inquiry. Instead of genuinely seeking truth, too many folks on both sides of the issue seem more concerned with figuring out who is on "my side" and who isn't. (I once witnessed an agnostic, Darwinist, psychologist get accused of being a "closet creationist" because he raised concerns about hasty attempts to explain various phenomena in Darwinian terms.) Placing aside stereotypes about "anti-science fundamentalists" and "anti-religion Darwinists," the Intelligent Design movement is important in two respects. First, it helps to remind us that not all of biology can be explained in terms of natural selection-as if biology didn't exist before Darwin. Second, Intelligent Design reminds us that intellectual inquiry does not have to begin and end with naturalism. I happen to think that methodological naturalism is a great place to start in the sciences, and we should get as much mileage out of it as we can. But not all of intellectual discovery lies in the methods and assumptions of the contemporary natural sciences. Along with cosmology, the Intelligent Design movement also illustrates that the borders of natural science are not always clear. Refusing to do scholarship that might cross conventional borders strikes me as unfruitful and cowardly.
7) Are your co-workers and associates from Young Life aware of your scholarly work in its details?
No. Though I have some supportive Young Life colleagues, Young Lifers don't generally read academic publications.
8) In his recent trilogy "The Victory of Reason," "For the Glory of God," and "One True God" Rodney Stark argues, in sum, that modernity as we know it (democracy, liberty, human rights, science, etc.) are necessarily preconditioned by the particular form of monotheism that Christianity promoted. Do you have any opinions as to the plausibility of such a suggestion?
Not having read Stark's trilogy, I had better not offer an opinion.
9) Do you anticipate a possible return to academia in a more full time capacity in the future?
I do indeed. I'm not ready to give details yet, but stay tuned.
10) If you had a chance to do it all over again what would you change about your education?
I believe I received a first rate education at Calvin College and then received excellent instruction and guidance from Frank Keil and the Keil - Spelke (Elizabeth) lab group at Cornell University. I have been asked if an education at a Christian college/university such as Calvin College is restricted and incomplete. The assumption seems to be that at such places there are some questions and perspectives that are taboo. I can not comment on all Christian universities, but my experience would support the opposite conclusion: at the good Christian universities you have fewer restrictions than at, say, major state universities in the United States. Professors at Calvin will present why evolution makes sense and where its weaknesses lie and how it might be reconciled with Christianity. At most secular universities, you will never hear various perspectives on evolution. At Calvin, you can grapple with philosophical arguments for and against theism. Even on matters of politics, the political science department at Calvin (and other such schools) represents more diversity than most state university departments. Perhaps the only change I would make in my education would be to have studied more philosophy of science. I see many cognitive and evolutionary scholars with rather weak understandings of science's philosophical foundations.
Labels: 10 questions
Steve says that Greg has a new theory about the hobbits of Flores. Anyone have a guess? I'm a lot less likely to believe they are what the Australian team says they are after the principal floated the idea they were from Australia. Call it conditional probability based on credibility.
You might want to check out Kate Wong's recent post over at Scientific American. My idea is that the hobbits were alien humanoids of some form who crash landed. This explains how they could be microcephalic and still produce twins: non-Terran cognitive packing is different. Ultimately their technology which reprocessed Terran food stuffs to be compatible with their own biochemistry broke down beyond repair and so they died off naturally. The next question is: where were they from?
Update: Suomalaiset ovat Neandertals (ja Conan O'Brien myĆ¶skin).
Update II: Cari lettori meridionali--come mai non bollite il manzo?
Update III: Thomar putki boro!
Update IV: Je m'appelle Robert. En garde!!! Animaux!
Addendum: Jaakkeli? Or neandertalinihminen?