gcochran

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[Link] The Coming Plague

Obviously you can limit travel in any way you want: you can let health workers go in and out while blocking regular travelers. Or, for that matter, you could block everyone under 20, everyone over 40, and everyone called Murphy. It does not have to be all or nothing.

If you were trying to make sense, you would let health workers fly in and quarantine them for three weeks on the way back: that's not much of an inconvenience, considering the risk. And you wouldn't let locals fly elsewhere for the duration.

" Liberia" was short hand: I mean the several countries in West Africa where the epidemic exists.

You know, discussions in this forum have a truly unusual flavor.

Q&A with Harpending and Cochran

Purges in Cambodia might have changed average genotypes because they hit such a high fraction of the population. Generally it's hard to change things much in one generation, though - particularly because of loose correlations between genotypes and dreadful political fates. In the future dictators should be better at this. Now if Stalin had taken all the smartest people in the Soviet Union and forcibly paired them up, artificially inflating assortative mating for intelligence, you would have seen an effect. If you were a billionaire, you could maybe bribe people into something similar.

Q&A with Harpending and Cochran

Paabo seems to think it unlikely that any of these introgressed alleles had a a significant selective advantage in humans, but that's unlikely. I'll bet money on this.

To be fair, I should explain why that is a sucker bet. John Hawks and I discussed about a situation with just a few tens of matings over all time: we were making the point that even in that minimal scenario, alleles with large advantages (on the order of 5%) could jump over to modern humans. The Max Planck estimate of 2% Neanderthal admixture is far more favorable to introgression: with that much of a start, and with at least 50,000 years to grow in, any allele with a selective advantage > 0.2% is likely to be over 50% today. Many such Neanderthal alleles should be fixed in Eurasians - or in some Eurasian populations in the right environments - or even in Africans, if the allele conferred global advantages. of course we'd have trouble proving this in Africans: the Science study really shows how much more Neanderthal ancestry Eurasians have than Africans, not the absolute amount in either population.

Note that the Fisher-wave velocity goes as the square root of the selective advantage: a Neanderthal allele with an advantage of 0.2% might have spread as far as the European lactase persistence variant, which probably had a selective advantage > 10%. Today we find that allele from north India, to Iceland, to the southern fringe of the Sahara.

Introgressing advantageous alleles derived from Neanderthals are probably more likely to go to fixation than most new favorable mutations. We now suspect that the majority of alleles that give large advantages to heterozygotes give smaller advantages to homozygotes and thus never go to fixation, using a variant of Fisher's geometric argument. In the long run they are replaced by alleles that work better in homozygotes and do go to fixation - but when we stole alleles from Neanderthals, we were mostly getting old tested ones, rather than flash-in-the-pan alleles like sickle-cell.

There had to be such advantageous alleles because Neanderthals had been in Europe and west Asia for hundreds of thousands of years - they were well-adapted to that different, non-African ecology.

When there is introgression between species, transmission of adaptive alleles seems to always happen. We know a lot about some cases: one good example is introgression in cattle. Taurine cattle were domesticated in the Middle East, Zebu cattle in India, from ancestral stocks that diverged about half a million years ago. Zebu genes have introgessed a lot into African taurine cattle, in part due to known advantages in heat/aridity tolerance and rinderpest resistance. Creeping zebuization has been going on the Middle East for thousands of years. If you go as far west as Egypt, cattle are about 25% Zebu in the nuclear genome, while you don't see anyzebu mtDNA or Y-chromosomes. This kind of discordance between the introgression of mtDNA/Y chromosomes and nuclear genomes is more common than not: looks like the same thing happened to us. Plausible when you think about it. Neanderthal mtDNA may well have had a selective disadvantage: they may have been blatant heat-wasters, since they had crummy clothing. Small population size might also have resulted in somewhat bunged up mtDNA, since selection is less efficient then.

Obviously some Neanderthal alleles had a selective disadvantage in humans, for example those that determined their different body form. Many more must have been effectively neutral, with no noticeable advantage over the version in anatomically modern humans. But some must have been useful - and the more useful they were, the more common they are today.

There seems to be a pattern in which an invasive species shows up, hangs around in an unspectacular way for sometime while it's picking up alleles from local sister species, and then spreads out irresistibly. We generally call those cosmopolitan species weeds.

Were some of those introgessing Neanderthal genes adaptive? Had to be. Do they account for the cultural big bang somewhat later? It would make sense, but it's not a lock. I'd call it likely.

Q&A with Harpending and Cochran
 There are sub-patterns.   There are facts about natural selection that every plant geneticist knows that few human geneticists will accept without a fight.  I mean, really, Henry, when a prominent human geneticist says " You don't really believe that bit about lactase persistence being selected, do you?" , or when someone even more famous asks "So why would there be more mutations in a bigger population?"  -  their minds ain't right. 
Q&A with Harpending and Cochran

I would say that it is some sense obvious that higher intelligence is possible, because the process that led to whatever intelligence we have was haphazard (path-dependent, stochastic, and all that) and because what optimization did occur was under severe constraints - some of which no longer apply. Clearly, the best possible performance under severe constraints is inferior to the best possible with fewer constraints.

So, if C-sections allow baby heads to get bigger, or if calories are freely available today, changes in brain development that take advantage of those relaxed constraints ought to be feasible. In principle this does not have to result in people who are damaged or goofy, although they would not do well in ancestral environments. In practice, since we won't know what the hell we are doing... of course it will.

Still, that's too close to an existence proof: it doesn't really tell you how to do it.

You could probably get real improvements by mining existing genetic variation: look at individuals and groups with unusually high IQs, search for causal variants. Plomin and company haven't any real success ( in terms of QTLs that explain much of the variance) but for this purpose one doesn't care about variance explained, just effect size. A rare allele that does the job would be useful. I'd look at groups with high average IQ, but at others also.

There are other possible approaches. If you could error-correct the genome, fix all the mutational noise, you might see higher IQ. You could dig up Gauss and clone him. My favorite idea is finding two human ethnic groups that 'nick' - whose F1 offspring exhibit hybrid vigor.

As for the singularity: I could, I think, make a pretty good case that scientific and technological progress is slowing down.

Q&A with Harpending and Cochran

Too random to have much effect, I should think. And at the same time, not awful enough to reduce the population to the point where drift would become important. Unless we're talking asteroid impacts.

One can imagine exceptions. For example, if alleles that gave resistance to some deadly plague had negative side effects on intelligence, then you'd see an effect. Note that negative side effects are much more likely than positive side effects.

I know of some neat anecdotal exceptions. Von Neumann got out of Germany in 1930, while the getting was good. When a friend said that Germany was oh-so-cultured and that there was nothing to worry about, Von Neumann didn't believe it. He started quoting the Melian dialogue - pointed out that the Athenians had been pretty cultured. High intelligence helped save his life.

Q&A with Harpending and Cochran

Hawks and I were talking about new genetic studies that showed a surprising number of sweeps, more than you'd expect from the long-term rate of change - and simultaneously noticed that there sure are a lot more people then there used to be - all potential mutants.

As for why someone didn't point this out earlier - say in 1930, when key results were available - I blame bad traditions in biology. Biologists mostly don't believe in theory: even when its predictions come true, they're not impressed.

My advantage, at least in part, comes from have had exactly one biology course in my entire life, which I took in the summer of my freshman year of high school, in a successful effort to avoid dissecting. If I ever write a scientific autobiography, it will be titled "Avoiding the Frog".

Q&A with Harpending and Cochran
 Better hunting techniques can significantly raise Malthusian limits. 

First, you have to remember that old-fashioned humans were one predator among many: improved hunting techniques could raise our share of the pot, as well as decreasing other predators' tendency to eat us. Also, modern humans seem to have used carcasses more efficiently than Neanderthals: they had permafrost storage pits and drying racks, so could have preserved meat for long periods. Neanderthals didn't, and I think they must have wasted a lot. Next, moderns used snares, traps, nets, bows etc to catch smaller game not much harvested by Neanderthals: they also made more use of fish and molluscs. And lastly, more plant foods. Altogether, their innovations gave them a larger share of the game, used that share more efficiently, tapped marine resources (lots of salmon in Europe), and harvested resources at a lower trophic level ( plants for example), which are always more abundant.

Hunting to extinction happened in some places, but not everywhere: it hardly happened in Africa at all. It happened most in places with no previous hominid occupation.

Implied population densities are, I think, extrapolations from known hunter gatherers, salted with some archeological info. Estimated densities range from 0.01/km sq to 1/km sq, strongly dependent upon resources. A lot like those of bears. Lower than chimps, probably: but then chimps manage with a lower-quality diet than humans. We're probably not as good at digesting leaves as they are.

Probably you have to consider Pleistocene climate as well: the world was generally nastier - colder, drier, lower plant productivity due to low CO2 levels.