Bake Sale

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1.  Mail a check, made out to West Hunter Incorporated.  Send it to

Gregory Cochran

6708 Loftus Ave, NE

Albuquerque, New Mexico 87109

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P.S. my Bitcoin address is  1Jv4cu1wETM5Xs9unjKbDbCrRF2mrjWXr5. Pronounced “mxyzptlk”

P.P.S. You can send money to me from a credit card (non-deductible) via Google Wallet to my gmail address (gregory.cochranATgmail.com)

Posted in Uncategorized | Tagged , | 33 Comments

Faster than Fisher

There’s a simple model of the spread of an advantageous allele:  You take σ, the typical  distance people move in one generation, and s,  the selective advantage: the advantageous allele spreads as a nonlinear wave at speed  σ * √(2s).  The problem is, that’s slow.   Suppose that s = 0.10 (a large advantage), σ = 10 kilometers, and a generation time of 30 years: the allele would take almost 7,000 years to expand out 1000 kilometers.

The European lactose-tolerance allele, T-13910 has spread much further than this model would predict. It’s found all over Europe ( very common in northern Europe) but is also found in South Asia (30%  in Pathans) and even in Africa (48% in Sudanese Fulani).

This big expansion didn’t just happen from peasants marrying the girl next door: it required migrations and conquests.  This one looks as if it rode with the Indo-European expansion: I’ll bet it started out in a group that had domesticated only horses.

The same processes, migration and conquest, must explain the wide distribution of many geographically widespread selective sweeps and partial sweeps.  They were adaptive, all right, but expanded much faster than possible from purely local diffusion.  We already have reason to think that SLC24A5 was carried to Europe by Middle Eastern farmers; the same is probably true for the haplotype that carries the high-activity ergothioniene transporter and the 35delG connexin-26/GJB2 deafness mutation. The Indo-Europeans probably introduced the T-13910 LCT mutation and the delta-F508 cystic fibrosis mutation,  so we should see delta-F508 in northwest India and Pakistan – and we do !

All these alleles had to confer an advantage, but population movements let them expand much farther and faster than girl-next-d0or ever could.

The same must be true for many of the European  variants influencing skin, eye, and hair color. Blue eyes seem to come from WHG (the mesolithic hunters); likely the wide distribution happened as people expanded (rapidly)  out of glacial refugia at the end of the Ice Age. Blond hair maps pretty well onto Corded Ware territory, which suggests that it came in with the Yamnaya. Blond, swarthy savages.   Red-heads? Bell Beakers.

As long as the conquerors incorporate even a moderate fraction (~20% ?) of the previous inhabitants, the sweeping genes cross over and can become common by the present. Given enough time, this can happen even with far lower levels of admixture, as seen with the adaptive alleles that originated in Neanderthals and Denisovans.

In a region without so many rapid, large-scale  expansions,  you won’t see adaptive alleles spread as rapidly.

Posted in Denisovans, Dietary adaptations, European Prehistory, Evolutionary Medicine, Genetics, Indo-European, Linguistics, Neanderthals, Skin color | Tagged | 67 Comments

The Greatest Generation

When you compare our trifling selves with the generation that landed in Normandy, invented the atomic bomb, and wrote The Big Sleep, it doesn’t look good. You could easily get the impression that the United States went straight from a Golden Age to one of cardboard, skipping silver and all the other metals.

But  when you consider that people must have had 48 chromosomes back then, rather than the current measly 46, much is explained.

Theophilus Painter, a prominent cytologist, had investigated human chromosome number in 1923. He thought that there were 24 in sperm cells, resulting in a count of 48, which is entirely reasonable. That is definitely the case for all our closest relatives (chimpanzees, bonobos, gorillas, and orangutans).

The authorities say that that Painter made a mistake, and that humans always had 46 chromosomes. But then, for 30 years after Painter’s work, the authorities said that people had 48.  Textbooks in genetics continued to say that Man has 48 chromosomes up until the mid 1950s.  Many cytologists and geneticists studied human chromosomes during that period, but they knew that there were 48, and that’s what they saw. Now they know that there are 46, and that’s what every student sees.

Either the authorities are fallible and most people are sheep, or human chromosome number actually changed sometime after World War II.  No one could believe the first alternative: it would hurt our feelings, and therefore cannot be true.  No, we have a fascinating result: people today are fundamentally different from the Greatest Generation, biologically different: we’re two chromosomes shy of a load. .    So it’s not our fault !

Posted in Genetics | 104 Comments

The Germ of Laziness

That happens to be the title of a pretty interesting book about hookworm in the US.  The book was fine, but the story is better.

Hookworms are parasitic nematodes that take up residence in the small intestine and drink your blood.  Getting there is complicated. Eggs are shed in the stool, hatch in to larvae in suitable soil, and enter the next host through bare feet. They then migrate (through the blood stream)  to the lungs, then to the trachea, where they are swallowed and eventually reach the small intestine.

Enough of them can cause significant blood loss and serious anemia.

They have been a particular problem among miners, wading in wet tunnels, and an epidemic among workers  in an Italian railway tunnel 1880 led to general medical understanding – other people had  figured some of this out earlier, sometimes much earlier (Theodor Bilharz, even Avicenna!) but that knowledge did not become general.

Charles Wardell Styles , who had studied  parasitology at the Institute Pasteur and gotten his Ph.D. at Leipzig, discovered that hookworm was common in the American South.  People thought differently in those days: he tried to abolish hookworm.  That was harder that he expected.  Southerners claimed that they couldn’t possibly have such a disgusting problem – it was just Yankee slander.  M.D.s ( back then, before the Flexner reforms, med school was often a six-month course) pointed out that he wasn’t even a doctor, so why should they listen to him?  After giving one talk, two M.D.s wondered if actually getting  rid of hookworm, curing the disease –  wouldn’t that cut into their practice?  And while he didn’t kill them on the spot, I guarantee he considered it.

Some company towns embraced hookworm eradication – they figured that outhouses and shoes were cheap, easily paid for by greater worker productivity. So various political types decided that he was a tool of the Interests, and therefore bad.

Somehow this idea reached the then-new Rockefeller foundation.  They did it right. They made sure that Charles Wardell Styles was not the public face of their effort – because he didn’t suffer fools gladly, and they needed someone who positively enjoyed them, someone who could get along with the general public. They went from town to town, rather like a revival, giving people fairly unpleasant chemicals that really did get rid of most of the hookworms. Since they are small( ~1 cm) and unspectacular, they kept dead giant roundworms (up to a foot long) in a bottle and pretended that they’d been expelled from the locals. They told people to use an outhouse and wear shoes – which led some  to claim that this was all an elaborate plot by John D. Rockefeller to sell shoes to innocent Southerners.  On the positive side, someone came up with the idea that the South would have won the War, except for hookworm : then worming folks was a tribute to the Lost Cause.

It worked.  Not perfectly, but well: greatly decreasing worm burden was good enough, since when it comes to hookworm, the dose makes the poison. A few may even be good for you, if you buy into the hygiene hypothesis.

There was another effect: it damaged the competitive position of black farmers.  They’re a good deal more resistant to hookworm (it came with them, probably), and hookworm resistance was likely one of the reasons for higher labor productivity among black farmers. Reducing and then eliminating malaria had the same effect.

Posted in Uncategorized | Tagged | 77 Comments

Déjà Vu all over again: America and Europe

In terms of social organization and technology, it seems to me that Mesolithic Europeans (around 10,000 years ago) were like archaic Amerindians before agriculture.  Many Amerindians on the west coast were still like that when Europeans arrived – foragers with bows and dugout canoes.

On the other hand,  the farmers of Old Europe were in important ways a lot like English settlers: the pioneers planted wheat, raised pigs and cows and sheep,  hunted deer, expanded and pushed aside the previous peoples, without much intermarriage.  Sure, Anglo pioneers were literate, had guns and iron, were part of a state, all of which gave them a much bigger edge over the Amerindians than Old Europe ever had over the Mesolithic hunter-gatherers and made the replacement about ten times faster – but in some ways it was similar. Some of this similarity was the product of historical accidents: the local Amerindians were thin on the ground, like Europe’s Mesolithic hunters – but not so much because farming hadn’t arrived (it had in most of the United States), more because of an ongoing population crash from European diseases.

On the gripping hand, the Indo-Europeans seem to have been something like the Plains Indians:  sure, they raised cattle rather than living off abundant wild buffalo, but they too were transformed into troublemakers by the advent of the horse. Both still did a bit of farming. They were also alike in that neither of them really knew what they were doing:  neither were the perfected product of thousands of years of horse nomadry.  The Indo-Europeans were the first raiders on horseback, and the Plains Indians had only been at it for a century, without any opportunity to learn state-of-the-art tricks from Eurasian horse nomads.

The biggest difference is that the Indo-Europeans won, while the Plains Indians were corralled into crappy reservations.

It turns out that all those Amerindians shared a fair amount of ancestry with the original Indo-Europeans (ANE, Sibermen), but that’s probably part of some cosmic joke for which we are the punchline.

 

 

Posted in Amerindians, European Prehistory, Indo-European | 99 Comments

The Evil Dead

Someone asked me to go over a chapter he wrote, about the impact of certain customs on human health. One of them was the health advantages of quick burial: the problem is, usually there aren’t any.   People seem to think that the organisms causing decomposition are pathogenic, but they’re not.  People killed by trauma (earthquakes,  floods, bullets) are dead enough, but not a threat.  Sometimes, the body of someone that died of an infectious disease is contagious – smallpox scabs have been known to remain infectious for a long, long time – but most causative agents are unable to survive for long after the host’s death. Now if you’re dissecting someone,  especially if they’re fresh, you probably don’t want to nick yourself with the scalpel – but if you just walk past the corpse and refrain from playing with it, you’re usually OK.

In the past, it may have been a good idea to bury people quickly, so as not to encourage a taste for human flesh in local predators, but that’s a somewhat indirect risk

Someone asked Lewis Thomas about the health risks of unburied bodies, with the intent of using a public-health threat as a legitimate reason to break the undertaker’s strike in New York – but the threat just wasn’t there. He said so, being an imperfectly political person.

 

Posted in Evolutionary Medicine | Tagged | 69 Comments

Remix

There is a new paper out in Science that analyzes the genome of a man (K14) that lived and died about 37,000 years ago, in Russia. They found that this individual came from a population that had shared ancestry with A.  Basal Eurasians, that mysterious population, sister to the main Out-of-Africa expansion and B. a population ancestral to both western hunter gatherers (WHG) and Ancient North Eurasians ( ANE, Sibermen).  In other words, a mix something like modern Europeans, but long, long ago.

Willerslev concludes that there was widespread intermingling back in the stone age: Western Asia was a metapopulation with repeated, possibly continuous gene flow, instead of a few discrete migration events.

The problem is that none of the other evidence agrees with this theory.  We’ve looked at the DNA of Mesolithic hunter-gatherers in Western hunter-gatherers – funny, they don’t have any Basal Eurasian mixture, or any ANE, either.  The Neolithic farmers of Europe have Basal Eurasian, but they don’t have any ANE, and although they have a component that is similar to the WHG, their uniparental lineages have almost no overlap with those of the western hunter-gatherers.  The 24,000-year-old Mal’ta skeleton  from Siberia is a good fit to ANE, but has no Basal Eurasian admixture. Moreover,  the Mesolithic and Neolithic samples are ~20,000 years later than K14.  If they were contemporaneous with K14, you could maybe argue that gene flow was common but just hadn’t reached them yet.  But they weren’t, and you can’t.

The thing is , you can mix two populations with distinct drift histories, and later detect the admixture event and say something about the original populations  – but you can’t unmix them – at least not by natural selection or drift, the only available processes in nature.

So Willerslev’s conclusion is wrong.  Moreover, we have plenty of evidence of serious migrations in Europe ( and elsewhere):  over time, the EEF expand and the Mesolithic hunters shrink. Later, all the villages in the Balkans are burned down, and all the houses in Germany and Poland disappear: sure looks as if someone came knocking.

What then is the real story?  Well, I see two possible explanations.  One is that there was was a small mixing event that produced a population with all three components – a population that wasn’t a major source of ancestry for later  populations. In the same way, if the daughter of a European Mesolithic hunter and a Basal Eurasian had married the son of an Ancient North Eurasian dude and a proto-Chinese chick in 10,000 BC, , they would have produced the world’s first Mexican, even if this complicated love-story happened thousands of years before Columbus. Still, one synthetic Mexican wouldn’t have mattered much – and it wouldn’t have meant that real, live Mexicans were descended from that early synthetic Mexican.  For that matter, although most of the people in Chile and Mexico are a mix of European and Amerindian, those two populations originated in separate admixture events.

The other possible explanation is error: they’ve made a mistake.  The genome quality is not all that good (2.42 X), and the fraction of genome recovered is not large – this might have made things more difficult.

Posted in Amerindians, European Prehistory, Indo-European | Tagged | 68 Comments