Since you asked…

Of course I believe in the importance of nature a bit more strongly than the average person. But our lives are still the sums of many different factors, some genetic, some nurture, some random. We also have something that feels like free will, crazy as that may sound; we are not doomed to eternally repeat the sins of our parents just because we saw them do something bad when we were three, nor are we condemned to robotically enact whatever flaws are encoded in our DNA. We are complicated.

I recently read a very interesting article about a man who discovered, via DNA testing, that his father (and grandfather) wasn’t really his father:

In the first phase, I was numb: no shock, anger, disappointment—just bewilderment. It was sohard to grasp. Unimaginable. It was hard to think clearly. And yet, a tiny bit of relief. Maybe truth would yield clarity and understanding of my father’s actions. This secondary sensation was the beginning of a wholly unexpected change in my internal being.

The second phase—feeling unmoored—was by far the hardest. Who am I? From where do I come? And who is this unknown man living in my body, coursing through my veins? I would subconsciously shake my hands trying to get him out of me. And worst, with my mother and the father who raised me both deceased, would I ever find the truth, get to the answers I was seeking? When you think you understand your origins, there is no obsessive need to explore and connect; you are satisfied knowing there is an origin and your ancestors and family members can be searched and contacted whenever needed. But when that assumption is taken away, you truly are an alien.

I should note that unlike Professor Schreiber, I had very decent parents; I have nothing to be ungrateful for beyond the normal vagaries of family life.

But the sense of being alien is still there; I always feel myself floating between worlds. There’s the world I was raised in, which I know culturally and can imitate quite effortlessly, (aside from a certain striver efficiency that seems more innate); then the world I talk to on the telephone, where people make the same sort of stupid mistakes as I do, but the cultural context is missing.

The advent of the internet is easing this gab, by the way, as the younger folks in my generation and I share more online culture.

Cultural things can get a good laugh out of you–you and someone else liked the same show, or went to the same park, or enjoyed the same brand of hot dogs–while innate things can strike very deep. Finding out that your brother got in trouble for the same distinct habits that you got in trouble for, or that you see in your own children, is really something. You look at this person and realize that despite this cultural and experiential gulf between you, you understand them–and they understand you.

The fellow in the article ended up with a bunch of new relatives, which he found very rewarding. For most adoptees, contacting biological family is iffy. People who gave you up when you were an infant may not want you in their lives, may not be good people, or may just be dead. But extended family never gave you up; extended family tends not to have all of that awkward parental baggage, either. They’re just potential siblings, aunts, uncles, cousins, etc., you’ve never met, and meeting them can be quite interesting.

I find that people really focus on adoptees’ parents, so I would just like to reiterate that biological families are more than just parents. They are cousins, grandparents, aunts, uncles, siblings, etc. They are entire families. Even people whose biological parents have given them good reason to never contact them (or are dead) may want to contact the rest of their biological families.

And like the good professor, I’ve found that meeting family from very different walks of life than my own has exposed me to very different perspectives. It is interesting seeing how similar people cope with very different situations–the things that stay the same (eg, dorkiness); the things that differ (attitudes toward guns).

Like they say, it’s about half nurture, half nature, half random chance, and half what you make of it.

(Just to be clear, yes, I know that’s not how halves work.)

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What does “Heritable” mean? 

“Heritable” (or “heritability”) has a specific and unfortunately non-obvious definition in genetics.

The word sounds like a synonym for “inheritable,” rather like your grandmother’s collection of musical clocks. Musical clocks are inheritable; fruit, since it rots, is not very inheritable.

This is not what “heritable” means.

“Heritability,” in genetics, is a measure of the percent of phenotypic variation within a population that can be attributed to genetics.

Let me clarify that in normal speak. “Phenotype” is something you can actually see about an organism, like how tall it is or the nest it builds. “Phenotypic variation” means things like “variation in height” or “variation in nest size.”

Let’s suppose we have two varieties of corn: a giant strain and a dwarf strain. If we plant them in a 100% even field with the same nutrients, water, sunlight, etc at every point in the field, then close to 100% of the variation in the resulting corn plants is genetic (some is just random chance, of course.)

In this population, then, height is nearly 100% heritable.

Let’s repeat the experiment, but this time, we sow our corn in an irregular field. Some patches have good soil; some have bad. Some spots are too dry or too wet. Some are sunny; others shaded. Etc.

Here it gets interesting, because aside from a bit of random chance in the distribution of seeds and environmental response, in most areas of the irregular field, our “tall” corn is still taller than the “short” corn. In the shady areas, both varieties don’t get enough sun, but the tall corn still grows taller. In the nutrient-poor areas, both varieties don’t get enough nutrients, but the tall still grows taller. But when we compare all of the corn all over the field, dwarf corn grown in the best areas grows taller than giant corn grown in the worst areas.

Our analysis of the irregular field leads us to conclude that water, sunlight, nutrients, and genes are all important in determining how tall corn gets.

Height in the irregular field is still heritable–genes are still important–but it is not 100% heritable, because other stuff is important, too.

What does it mean to be 10, 40, or 80% heritable?

If height is 10% heritable, then most of the variety in height you see is due to non-genetic factors, like nutrition. Genes still have an effect–people with tall genes will still, on average, be taller–but environmental effects really dominate–perhaps some people who should have been tall are severely malnourished.

In modern, first world countries, height is about 80% heritable–that is, since most people in first world countries get plenty of food and don’t catch infections that stunt their growth, most of the variation we see is genetic. In some third world countries, however, the heritability of height drops to 65%. These are places where many people do not get the nutrients they need to achieve their full genetic potential.

How do you achieve 0% heritability?

A trait is 0% heritable not if you can’t inherit it, but if genetics explains none of the variation in the sample. Suppose we seeded an irregular field entirely with identical, cloned corn. The height of the resulting corn would would vary from area to area depending on nutrients, sunlight, water, etc. Since the original seeds were 100% genetically identical, all of the variation is environmental. Genes are, of course, important to height–if the relevant genes disappeared from the corn, it would stop growing–but they explain none of the variation in this population.

The heritability of a trait decreases, therefore, as genetic uniformity increases or the environment becomes more unequal. Heritability increases as genetics become more varied or the environment becomes more equal. 

Note that the genes involved do not need to code directly for the trait being measured. The taller people in a population, for example, might have lactase persistence genes, which let them extract more calories from the milk they drink than their neighbors. Or they might be thieves who steal food from their neighbors.

I remember a case where investigators were trying to discover why most of the boys at an orphanage had developed pellagra, then a mystery disease, but some hadn’t. It turns out that the boys who hadn’t developed it were sneaking into the kitchen at night and stealing food.

Pellagra is a nutritional deficiency caused by lack of niacin, aka B3. Poor Southerners used to come down with it from eating diets composed solely of (un-nixtamalized) corn for months on end.

The ultimate cause of pellagra is environmental–lack of niacin–but who comes down with pellagra is at least partially determined by genes, because genes influence your likelihood of eating nothing but corn for 6 months straight. Sociopaths who steal the occasional ham, for example, won’t get pellagra, but sociopaths who get caught and sent to badly run prisons, however, increase their odds of getting it. In general, smart people who work hard and earn lots of money significantly decrease their chance of getting it, but smart black people enslaved against their will are more likely to get it. So pellagra is heritable–even though it is ultimately a nutritional deficiency.

What’s the point of heritability?

If you’re breeding corn (or cattle,) it helps to know whether, given good conditions, you can hope to change a trait. Traits with low heritability even under good conditions simply can’t be affected very much by breeding, while traits with high heritability can.

In humans, heritability helps us seek out the ultimate causes of diseases. On a social level, it can help measure how fair a society is, or whether the things we are doing to try to make society better are actually working.

For example, people would love to find a way to make children smarter. From Baby Einstein to HeadStart, people have tried all sorts of things to raise IQ. But beyond making sure that everyone has enough to eat, no nutrient deficiencies, and some kind of education, few of these interventions seem to make much difference.

Here people usually throw in a clarification about the difference between “shared” and “non-shared” environment. Shared environment is stuff you share with other members of your population, like the house your family lives in or the school you and your classmates attend. Non-shared is basically “random stuff,” like the time you caught meningitis but your twin didn’t.

Like anything controversial, people of course argue about the methodology and mathematics of these studies. They also argue about proximate and ultimate causes, and get caught up matters of cultural variation. For example, is wearing glasses heritable? Some would say that it can’t be, because how can you inherit a gene that somehow codes for possessing a newly invented (on the scale of human evolutionary history) object?

But this is basically a fallacy that stems from mixing up proximate and ultimate causes. Obviously there is no gene that makes a pair of glasses grow out of your head, nor one that makes you feel compelled to go and buy them. It is also obvious that not all human populations throughout history have had glasses. But within a population that does have glasses, the chances of you wearing glasses is strongly predicted by whether or not you are nearsighted, and nearsightedness is a remarkable 91% heritable. 

Of course, some nearsighted people opt to wear contact lenses, which lowers the heritability estimate for glasses, but the signal is still pretty darn strong, since almost no one who doesn’t have vision difficulties wears glasses.

If we expand our sample population to include people who lived before the invention of eyeglasses, or who live in countries where most people are too poor to afford glasses, then our heritability estimate will drop quite a bit. You can’t buy glasses if they don’t exist, after all, no matter how bad your eyesight it. But the fact that glasses themselves are a recent artifact of particular human cultures does not change the fact that, within those populations, wearing glasses is heritable.

“Heritability” does not depend on whether there is (or we know of ) any direct mechanism for a gene to code for the thing under study. It is only a statistical measure of genetic variation that correlates with the visible variation we’re looking at in a population.

I hope this helps.

Book Club: The 10,000 Year Explosion pt 7: Finale

 

Niels Bohr
Niels Bohr: 50% Jewish, 100% Quantum Physics

Chapter 7 of The 10,000 Year Explosion is about the evolution of high Ashkenazi IQ; chapter 8 is the Conclusion, which is just a quick summary of the whole book. (If you’re wondering if you would enjoy the book, try reading the conclusion and see if you want to know more.)

This has been an enjoyable book. As works on human evolution go, it’s light–not too long and no complicated math. Pinker’s The Blank Slate gets into much more philosophy and ethics. But it also covers a lot of interesting ground, especially if you’re new to the subject.

I have seen at least 2 people mention recently that they had plans to respond to/address Cochran and Harpending’s timeline of Jewish history/evolution in chapter 7. I don’t know enough to question the story, so I hope you’ll jump in with anything enlightening.

The basic thesis of Chapter 7 is that Ashkenazi massive over-representation in science, math, billionaires, and ideas generally is due to their massive brains, which is due in turn to selective pressure over the past thousand years or so in Germany and nearby countries to be good at jobs that require intellect. The authors quote the historian B. D. Weinryb:

More children survived to adulthood in affluent families than in less affluent ones. A number of genealogies of business leaders, prominent rabbis, community leaders, and the like–generally belonging to the more affluent classes–show that such people often had four, six, sometimes even eight or nice children who reached adulthood…

800px-Niels_Bohr_Albert_Einstein_by_Ehrenfest
Einstein and Bohr, 1925

Weinryb cites a census of the town of Brody, 1764: homeowner household had 1.2 children per adult; tenant households had only 0.6.

As evidence for this recent evolution, the authors point to the many genetic diseases that disproportionately affect Ashkenazim:

Tay-Sachs disease, Gaucher’s disease, familial dysautonomia, and two different forms of hereditary breast cancer (BRCA1 and BRCA2), and these diseases are up to 100 times more common in Ashkenazi Jews than in other European populations. …

In principle, absent some special cause, genetic diseases like these should be rare. New mutations, some of which have bad effects, appear in every generation, but those that cause death or reduced fertility should be disappearing with every generation. … one in every twenty-five Ashkenazi Jews carries a copy of the Tay-Sachs mutation, which kills homozygotes in early childhood. This is an alarming rate.

What’s so special about these diseases, and why do the Ashkenazim have so darn many of them?

Some of them look like IQ boosters, considering their effects on the development of the central nervous system. The sphingolipid mutations, in particular, have effects that could plausibly boost intelligence. In each, there is a buildup of some particular sphingolipid, a class of modified fat molecules that play a role in signal transmission and are especially common in neural tissues. Researchers have determined that elevated levels of those sphingolipids cause the growth of more connections among neurons..

There is a similar effect in Tay-Sachs disease: increased levels of a characteristic storage compound… which causes a marked increase in the growth of dendrites, the fine branches that connect neurons. …

We looked at the occupations of patients in Israel with Gaucher’s disease… These patients are much more likely to be engineers or scientists than the average Israeli Ashkenazi Jew–about eleven times more likely, in fact.

Einstein_oppenheimer
Einstein and Oppenheimer, Father of the Atomic Bomb, c. 1950

Basically, the idea is that similar to sickle cell anemia, being heterozygous for one of these traits may make you smarter–and being homozygous might make your life considerably shorter. In an environment where being a heterozygous carrier is rewarded strongly enough, the diseases will propagate–even if they incur a significant cost.

It’s a persuasive argument.

I’d like to go on a quick tangent to Von Neumann’s Wikipedia page:

Von Neumann was a child prodigy. When he was 6 years old, he could divide two 8-digit numbers in his head [14][15] and could converse in Ancient Greek. When the 6-year-old von Neumann caught his mother staring aimlessly, he asked her, “What are you calculating?”[16]

Children did not begin formal schooling in Hungary until they were ten years of age; governesses taught von Neumann, his brothers and his cousins. Max believed that knowledge of languages in addition to Hungarian was essential, so the children were tutored in English, French, German and Italian.[17] By the age of 8, von Neumann was familiar with differential and integral calculus,[18] but he was particularly interested in history. He read his way through Wilhelm Oncken‘s 46-volume Allgemeine Geschichte in Einzeldarstellungen.[19] A copy was contained in a private library Max purchased. One of the rooms in the apartment was converted into a library and reading room, with bookshelves from ceiling to floor.[20]

JohnvonNeumann-LosAlamos
Von Neumann

Von Neumann entered the Lutheran Fasori Evangélikus Gimnázium in 1911. Wigner was a year ahead of von Neumann at the Lutheran School and soon became his friend.[21] This was one of the best schools in Budapest and was part of a brilliant education system designed for the elite. Under the Hungarian system, children received all their education at the one gymnasium. Despite being run by the Lutheran Church, the school was predominately Jewish in its student body [22] The school system produced a generation noted for intellectual achievement, which included Theodore von Kármán (b. 1881), George de Hevesy (b. 1885), Leó Szilárd (b. 1898), Dennis Gabor (b. 1900), Eugene Wigner (b. 1902), Edward Teller (b. 1908), and Paul Erdős (b. 1913).[23] Collectively, they were sometimes known as “The Martians“.[24] 

One final thing in The 10,000 Year Explosion jumped out at me:

There are also reports of individuals with higher-than-average intelligence who have nonclassic congenital adrenal hyperplasia (CAH)… CAH, which causes increased exposure of the developing fetus to androgens (male sex hormones), is relatively mild compared to diseases like Tay-Sachs. At least seven studies show high IQ in CAH patients, parents, and siblings, ranging from 107 to 113. The gene frequency of CAH among the Ashkenazim is almost 20 percent.

Holy HBD, Batman, that’ll give you a feminist movement.

If you haven’t been keeping obsessive track of who’s who in the feminist movement, many of the early pioneers were Jewish women, as discussed in a recent article by the Jewish Telegraph Agency, “A History of the Radical Jewish Feminists and the one Subject they Never Talked About“:

Heather Booth, Amy Kesselman, Vivian Rothstein and Naomi Weisstein. The names of these bold and influential radical feminists may have faded in recent years, but they remain icons to students of the women’s liberation movement …

The Gang of Four, as they dubbed themselves, were among the founders of Chicago’s Women’s Liberation Union. …

Over weeks, months and years, no subject went unturned, from the political to the sexual to the personal. They were “ready to turn the world upside down,” recalled Weisstein, an influential psychologist, neuroscientist and academic who died in 2015.

But one subject never came up: the Jewish backgrounds of the majority of the group.

“We never talked about it,” Weisstein said.

Betty Friedan was Jewish; Gloria Steinem is half Jewish. There are a lot of Jewish feminists.

Of course, Jews are over-represented in pretty much every intellectual circle. Ayn Rand, Karl Marx, and Noam Chomsky are all Jewish. Einstein and Freud were Jewish. I haven’t seen anything suggesting that Jews are more over-represented in feminism than in any other intellectual circle they’re over-represented in. Perhaps they just like ideas. Someone should come up with some numbers.

Here’s a page on Congenital Adrenal Hyperplasia. The “classic” variety is often deadly, but the non-classic (the sort we are discussing here) doesn’t kill you.

Paul_Erdos_with_Terence_Tao
Paul Erdős with Terrence Tao, 1984 (Tao isn’t Jewish, of course.)

I’ve long suspected that I know so many trans people because some intersex conditions result in smarter brains (in this case, women who are better than average at math.) It looks like I may be on the right track.

Well, that’s the end of the book. I hope you enjoyed it. What did you think? And what should we read next? (I’m thinking of doing Pinker’s Blank Slate.)

Book Club: The 10,000 Year Explosion: pt 5: Gene Flow

Genghis Khan, spreader of genes

Welcome back to the book club. Today we’re discussing Chapter 5 of The 10,000 Year Explosion, Gene Flow. In this chapter, Greg and Henry discuss some of the many ways genes can (and sometimes can’t) get around.

You know, sometimes it is difficult to think of something really interesting to say in reaction to something I’ve read. Sometimes I just think it is very interesting, and hope others find it so, too. This is one of those chapters.

So today I decided to read the papers cited in the chapter, plus a few more related papers on the subject.

High-Resolution SNPs and Microsatellite Haplotypes point to a single, Recent Entry of Native American Y Chromosomes into the Americas

Single-nucleotide polymorphism (SNP) analysis indicated that three major haplogroups, denoted as C, Q, and R, accounted for nearly 96% of Native American Y chromosomes. Haplogroups C and Q were deemed to represent early Native American founding Y chromosome lineages; however, most haplogroup R lineages present in Native Americans most likely came from recent admixture with Europeans. Although different phylogeographic and STR diversity patterns for the two major founding haplogroups previously led to the inference that they were carried from Asia to the Americas separately, the hypothesis of a single migration of a polymorphic founding population better fits our expanded database. Phylogenetic analyses of STR variation within haplogroups C and Q traced both lineages to a probable ancestral homeland in the vicinity of the Altai Mountains in Southwest Siberia. Divergence dates between the Altai plus North Asians versus the Native American population system ranged from 10,100 to 17,200 years for all lineages, precluding a very early entry into the Americas.

However, Asymmetric Male and Female Genetic Histories among Native Americans from Eastern North America

We found that sociocultural factors have played a more important role than language or geography in shaping the patterns of Y chromosome variation in eastern North America. Comparisons with previous mtDNA studies of the same samples demonstrate that male and female demographic histories differ substantially in this region. Postmarital residence patterns have strongly influenced genetic structure, with patrilocal and matrilocal populations showing different patterns of male and female gene flow. European contact also had a significant but sex-specific impact due to a high level of male-mediated European admixture. Finally, this study addresses long-standing questions about the history of Iroquoian populations by suggesting that the ancestral Iroquoian population lived in southeastern North America.

And in Mexico, your different racial mix has something to do with your risk of Type 2 Diabetes, but you know, race is a social construct or something:

Type 2 diabetes (T2D) is at least twice as prevalent in Native American populations as in populations of European ancestry, so admixture mapping is well suited to study the genetic basis of this complex disease. We have characterized the admixture proportions in a sample of 286 unrelated T2D patients and 275 controls from Mexico City and we discuss the implications of the results for admixture mapping studies. … The average proportions of Native American, European and, West African admixture were estimated as 65, 30, and 5%, respectively. The contributions of Native American ancestors to maternal and paternal lineages were estimated as 90 and 40%, respectively. In a logistic model with higher educational status as dependent variable, the odds ratio for higher educational status associated with an increase from 0 to 1 in European admixture proportions was 9.4 (95%, credible interval 3.8-22.6). This association of socioeconomic status with individual admixture proportion shows that genetic stratification in this population is paralleled, and possibly maintained, by socioeconomic stratification. The effective number of generations back to unadmixed ancestors was 6.7 (95% CI 5.7-8.0)…

In other words, Conquistador men had children with a lot of the local ladies. 

Oh hey, while we’re at it: 

The Genomic Landscape of Western South America: 

Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here we explore the genetic structure of 177 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, with a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long distance genetic connections between speakers of the same language family suggest that languages had spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. 

In other news: 

Strong Selective Sweep Before 45,000 BP Displaced Archaic Admixture Across the X Chromosome

The X chromosome in non-African populations has less diversity and less Neanderthal introgression than expected. We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust’-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event.

Why not a later out-of-Africa event? Or a simultaneous event that just happened not to mate with Neanderthals? Or sweeps on the X chromosome that happened to remove Neanderthal DNA due to Neanderthal and X being really incompatible? I don’t know. 

The Neolithic Invasion of Europe:

Who are Europeans? Both prehistoric archaeology and, subsequently, classical population genetics have attempted to trace the ancestry of modern Europeans back to the first appearance of agriculture in the continent; however, the question has remained controversial. Classical population geneticists attributed the major pattern in the European gene pool to the demographic impact of Neolithic farmers dispersing from the Near East, but archaeological research has failed to uncover substantial evidence for the population growth that is supposed to have driven this process. … Both mitochondrial DNA and Y-chromosome analyses have indicated a contribution of Neolithic Near Eastern lineages to the gene pool of modern Europeans of around a quarter or less. This suggests that dispersals bringing the Neolithic to Europe may have been demographically minor and that contact and assimilation had an important role.

I wouldn’t call a quarter “minor.” But it is true that the Anatolian farming people who invaded Europe didn’t kill off all of the locals, and then later Europe was invaded by the non-Anatolian, Indo-European people. 

Revealing the prehistoric settling of Australia by Y chromosome and mtDNA analysis

(i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa ≈50–70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event ≈50,000 years ago, … (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged ≈8,000 years ago…

Aboriginal Australian mitochondrial genome variation

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. … We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene.

Meanwhile, in Indonesia

We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.

I liked the quote from Jared Diamond (say what you will about him, I like Diamond. He at least tries hard to tackle difficult questions):  

“When I was living among Elopi tribespeople in west New Guinea and wanted to cross the territory of the neighboring Fayu tribe in order to reach a nearby mountain, the Elopis explained tome matter-of-factly that the Fayus would kill me if I tried. From a New Guinea perspective, it seemed so perfectly natural and self-explanatory. Of course the Fayus will kill any trespasser…”

This is why people often claim that we moderns are the WEIRDOs. 

Evidence that Alexander the Great got around (the world)–Y-Chromosomal Evidence for a Limited Greek Contribution to the Pathan population of Pakistan

Three Pakistani populations residing in northern Pakistan, the Burusho, Kalash and Pathan claim descent from Greek soldiers associated with Alexander’s invasion of southwest Asia. … In pairwise comparisons between the Greeks and the three Pakistani populations using genetic distance measures sensitive to recent events, the lowest distances were observed between the Greeks and the Pathans. Clade E3b1 lineages, which were frequent in the Greeks but not in Pakistan, were nevertheless observed in two Pathan individuals, one of whom shared a 16 Y-STR haplotype with the Greeks. The worldwide distribution of a shortened (9 Y-STR) version of this haplotype, determined from database information, was concentrated in Macedonia and Greece, suggesting an origin there. Although based on only a few unrelated descendants this provides strong evidence for a European origin for a small proportion of the Pathan Y chromosomes.

Of course, who can discuss genetic spread without mentioning that lord of men, Genghis Khan? 

We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: ∼8% of the men in this region carry it, and it thus makes up ∼0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia ∼1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.

“Novel” lol. 

And finally, Blue Eyes

Several studies have shown that the OCA2 locus is the major contributor to the human eye color variation. By linkage analysis of a large Danish family, we finemapped the blue eye color locus to a 166 Kbp region within the HERC2 gene. … The brown eye color allele of rs12913832 is highly conserved throughout a number of species. … One single haplotype, represented by six polymorphic SNPs covering half of the 3′ end of the HERC2 gene, was found in 155 blue-eyed individuals from Denmark, and in 5 and 2 blue-eyed individuals from Turkey and Jordan, respectively. Hence, our data suggest a common founder mutation in an OCA2 inhibiting regulatory element as the cause of blue eye color in humans. In addition, an LOD score of Z = 4.21 between hair color and D14S72 was obtained in the large family, indicating that RABGGTA is a candidate gene for hair color.

What about you? What did you think of this chapter?

Two Denisovan Admixture Events?

Recent genetic analysis suggests that humans mated with the mysterious Denisovans not once, but twice

Asian genomes carry introgressed DNA from Denisovans and Neanderthals

East Asians show evidence of introgression from two distinct Denisovan populations

South Asians and Oceanians carry introgression from one Denisovan population

I can’t read the whole paper, because it’s paywalled, but if correct, this is quite the change. Previously, only small amounts of Denisovan were detected in East Asians, while large amounts (2-6%) were detected in Oceanians (ie, Melanesians, Papuans, and Australian Aborigines.) 

According to Wikipedia:

Statistical analysis of genomic DNA sequences from different Asian populations indicates that at least two distinct populations of Denisovans existed,[50][51] and that a second introgression event from Denisovans into humans occurred. A study of Han ChineseJapanese and Dai genomes revealed that modern East Asian populations include two Denisovan DNA components: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from the Altai cave. These components were interpreted as representing separate introgression events involving two divergent Denisovan populations. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians, but this DNA only came from the same single Denisovan introgression seen in Papuans.[52]  …

The Denisovans, in case you’re new here, are a human species similar to the Neanderthals who lived… well, we’re not sure exactly where they lived, other than the Altai Cave, Siberia. We also don’t know what they looked like, because we have only found a few of their bones–a finger bone and some teeth–but they might have looked a bit like the Red Deer Cave People. Remarkably, though, these were in good enough condition (Siberia preserves things very well,) to allow scientists to extract sufficient DNA to determine that they are indeed a human species, but one that split from the ancestors of Homo sapiens about 600,000-750,000 years ago, and from the Neanderthals about 200,000 years later. 

Just as Homo sapiens mated with Neanderthals, so Denisovans mated with Neanderthals and Homo sapiens–the human family tree is growing increasingly complex. 

We don’t know exactly where these interbreeding events happened, since we know so little about the Denisovans (at least one of the Neanderthal interbreeding events probably happened in the Middle East, given that all non-Africans [and some Africans] have Neanderthal DNA,) but a clue lies in the DNA of the Negrito peoples. 

The Negritoes are a variety of peoples who live in south east Asia and, like the Pygmies of Africa, are rather short. Some of them, like the Aeta of the Philippines, have almost Papuan levels of Denisovan admixture, while others, like the Onge of India, have almost none. Assuming the Negritos are related to each other and not just isolated examples of island dwarfism, this suggests that the interbreeding event really did take places somewhere east of the major Indonesian islands of Sumatra and Borneo (which probably weren’t islands at the time, but connected to the mainland). The Denisovans may have been clever enough to build boats and cross the Wallace Line, surviving in the more isolated islands of Indonesia and the Philippines. 

On a related note, the article I just linked to from John Hawks, “This is where Scientists Might Find the Next Hobbits,” is truly excellent: 

In May, an international team of scientists led by Thomas Ingicco revealed new archaeological findings from Kalinga, in the northernmost part of Luzon, Philippines. Until now, scientists have mostly assumed that the Philippines were first inhabited by modern humans, only after 100,000 years ago. But the artifacts unearthed by Ingicco and coworkers were much older, more than 700,000 years old. …

Luzon was never connected to the Asian mainland, even when sea level was at its lowest during the Ice Ages. To get there, ancient hominins had to float. Who were they, and how did they get there?

Timeline of ancient Indonesian and Filipino hominin findings, from John Hawks’s article

I recommend you read the whole thing.

What’s all of this Denisovan DNA good for, anyway? Quoting Wikipedia again:

The immune system’s HLA alleles have drawn particular attention in the attempt to identify genes that may derive from archaic human populations. Although not present in the sequenced Denisova genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles has led to the suggestion that it introgressed from Denisovans into humans in west Asia. As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of Denisovan or Neanderthal origin.[54] The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population. A higher-quality Denisovan genome published in 2012 reveals variants of genes in humans that are associated with dark skin, brown hair, and brown eyes – consistent with features found with Melanesians today.[16] A study involving 40 Han Chinese and 40 people of ethnic Tibetan background identified a region of DNA around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude found in Tibetans is also found in the Denisovan genome.[55][56] In Papuans, introgressed Neanderthal alleles have highest frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissues.[57]

It is a great era in genetics. 

The Female Problem

 

800px-otto_hahn_und_lise_meitner
Lise Meitner and Otto Hahn in their laboratory, 1912

As Pumpkin Person reports, 96% of people with math IQs over 154 are male (at least in the early 1980s.) Quoting from  Feingold, A. (1988). Cognitive gender differences are disappearing. American Psychologist, 43(2), 95-103:

When the examinees from the two test administrations were combined, 96% of 99 scores of 800 (the highest possible scaled score), 90% of 433 scores in the 780-790 range, 81% of 1479 scores between 750 and 770, and 56% of 3,768 scores of 600 were earned by boys.

The linked article notes that this was an improvement over the previous gender gap in high-end math scores. (This improvement may itself be an illusion, due to the immigration of smarter Asians rather than any narrowing of the gap among locals.)

I don’t know what the slant is among folks with 800s on the verbal sub-test, though it is probably less–far more published authors and journalists are male than top mathematicians are female. (Language is a much older human skill than math, and we seem to have a corresponding easier time with it.) ETA: I found some data. Verbal is split nearly 50/50 across the board; the short-lived essay had a female bias. Since the 90s, the male:female ratio for scores over 700 improved from 13:1 to 4:1; there’s more randomness in the data for 800s, but the ratio is consistently more male-dominated.

High SAT (or any other sort of) scores is isolating. A person with a combined score between 950 and 1150 (on recent tests) falls comfortably into the middle of the range; most people have scores near them. A person with a score above 1350 is in the 90th%–that is, 90% of people have scores lower than theirs.

People with scores that round up to 1600 are above the 99th%. Over 99% of people have lower scores than they do.

And if on top of that you are a female with a math score above 750, you’re now a minority within a minority–75% or more of the tiny sliver of people at your level are likely to be male.

Obviously the exact details change over time–the SAT is periodically re-normed and revised–and of course no one makes friends by pulling out their SAT scores and nixing anyone with worse results.

But the general point holds true, regardless of our adjustments, because people bond with folks who think similarly to themselves, have similar interests, or are classmates/coworkers–and if you are a female with high math abilities, you know well that your environment is heavily male.

This is not so bad if you are at a point in your life when you are looking for someone to date and want to be around lots of men (in fact, it can be quite pleasant.) It becomes a problem when you are past that point, and looking for fellow women to converse with. Married women with children, for example, do not typically associate in groups that are 90% male–nor should they, for good reasons I can explain in depth if you want me to.

A few months ago, a young woman named Kathleen Rebecca Forth committed suicide. I didn’t know Forth, but she was a nerd, and nerds are my tribe.

She was an effective altruist who specialized in understanding people through the application of rationality techniques. She was in the process of becoming a data scientist so that she could earn the money she needed to dedicate her life to charity.

I cannot judge the objective truth of Forth’s suicide letter, because I don’t know her nor any of the people in her particular communities. I have very little experience with life as a single person, having had the good luck to marry young. Nevertheless, Forth is dead.

At the risk of oversimplifying the complex motivations for Forth’s death, she was desperately alone and felt like she had no one to protect her. She wanted friends, but was instead surrounded by men who wanted to mate with her (with or without her consent.) Normal people can solve this problem by simply hanging out with more women. This is much harder for nerds:

Rationality and effective altruism are the loves of my life. They are who I am.

I also love programming. Programming is part of who I am.

I could leave rationality, effective altruism and programming to escape the male-dominated environments that increase my sexual violence risk so much. The trouble is, I wouldn’t be myself. I would have to act like someone else all day.

Imagine leaving everything you’re interested in, and all the social groups where people have something in common with you. You’d be socially isolated. You’d be constantly pretending to enjoy work you don’t like, to enjoy activities you’re not interested in, to bond with people who don’t understand you, trying to be close to people you don’t relate to… What kind of life is that? …

Before I found this place, my life was utterly unengaging. No one was interested in talking about the same things. I was actually trying to talk about rationality and effective altruism for years before I found this place, and was referred into it because of that!

My life was tedious and very lonely. I never want to go back to that again. Being outside this network felt like being dead inside my own skin.

Why Forth could not effectively change the way she interacted with men in order to decrease the sexual interest she received from them, I do not know–it is perhaps unknowable–but I think her life would not have ended had she been married.

A couple of years ago, I met someone who initiated a form of attraction I’d never experienced before. I was upset because of a sex offender and wanted to be protected. For months, I desperately wanted this person to protect me. My mind screamed for it every day. My survival instincts told me I needed to be in their territory. This went on for months. I fantasized about throwing myself at them, and even obeying them, because they protected me in the fantasy.

That is very strange for me because I had never felt that way about anyone. Obedience? How? That seemed so senseless.

Look, no one is smart in all ways at once. We all have our blind spots. Forth’s blind spot was this thing called “marriage.” It is perhaps also a blind spot for most of the people around her–especially this one. She should not be condemned for not being perfect, any more than the rest of us.

But we can still conclude that she was desperately lonely for normal things that normal people seek–friendship, love, marriage–and her difficulties hailed in part from the fact that her environment was 90% male. She had no group of like-minded females to bond with and seek advice and feedback from.

Forth’s death prompted me to create The Female Side, an open thread for any female readers of this blog, along with a Slack-based discussion group. (The invite is in the comments over on the Female Side.) You don’t have to be alone. (You don’t even have to be good at math.) We are rare, but we are out here.

(Note: anyone can feel free to treat any thread as an Open Thread, and some folks prefer to post over on the About page.)

Given all of this, why don’t I embrace efforts to get more women into STEM? Why do I find these efforts repulsive, and accept the heavily male-dominated landscape? Wouldn’t it be in my self-interest to attract more women to STEM and convince people, generally, that women are talented at such endeavors?

I would love it if more women were genuinely interested in STEM. I am also grateful to pioneers like Marie Curie and Lise Meitner, whose brilliance and dedication forced open the doors of academies that had formerly been entirely closed to women.

The difficulty is that genuine interest in STEM is rare, and even rarer in women. The over-representation of men at both the high and low ends of mathematical abilities is most likely due to biological causes that even a perfect society that removes all gender-based discrimination and biases cannot eliminate.

It does not benefit me one bit if STEM gets flooded with women who are not nerds. That is just normies invading and taking over my territory. It’s middle school all over again.

If your idea of “getting girls interested in STEM” includes makeup kits and spa masks, I posit that you have no idea what you’re talking about, you’re appropriating my culture, and you can fuck off.

Please take a moment to appreciate just how terrible this “Project Mc2” “Lip Balm Lab” is. I am not sure I have words sufficient to describe how much I hate this thing and its entire line, but let me try to summarize:

There’s nothing inherently wrong with lib balm. The invention of makeup that isn’t full of lead and toxic chemicals was a real boon to women. There are, in fact, scientists at work at makeup companies, devoted to inventing new shades of eye shadow, quicker-drying nail polish, less toxic lipstick, etc.

And… wearing makeup is incredibly normative for women. Little girls play at wearing makeup. Obtaining your first adult makeup and learning how to apply it is practically a rite of passage for young teens. Most adult women love makeup and wear it every day.

Except:

Nerd women.

Female nerds just aren’t into makeup.

Marie Curie
Marie Curie, fashionista

I’m not saying they never wear makeup–there’s even a significant subculture of people who enjoy cosplay/historical re-enactment and construct elaborate costumes, including makeup–but most of us don’t. Much like male nerds, we prioritize comfort and functionality in the things covering our bodies, not fashion trends.

And if anything, makeup is one of the most obvious shibboleths that distinguishes between nerd females and normies.

In other words, they took the tribal marker of the people who made fun of us throughout elementary and highschool and repackaged it as “Science!” in an effort to get more normies into STEM, and I’m supposed to be happy about this?!

I am not ashamed of the fact that women are rarer than men at the highest levels of math abilities. Women are also rarer than men at the lowest levels of math abilities. I feel no need to cram people into disciplines they aren’t actually interested in just so we can have equal numbers of people in each–we don’t need equal numbers of men and women in construction work, plumbing, electrical engineering, long-haul trucking, nursing, teaching, childcare, etc.

It’s okay for men and women to enjoy different things–on average–and it’s also okay for some people to have unusual talents or interests.

It’s okay to be you.

(I mean, unless you’re a murderer or something. Then don’t be you.)

Book Club: The 10,000 Year Explosion, Part 3

940px-Centres_of_origin_and_spread_of_agriculture.svg
The spread of agriculture

Welcome back to the Book Club. Today we’re reading Chapter 3: Agriculture, from Cochran and Harpending’s The 10,000 Year Explosion: How Civilization Accelerated Human Evolution.

One of my fine readers asked for “best of” recommendations for Cochran and Harpending’s blog, West Hunter. This is a good question, and as I have not yet found a suitable list, I thought I would make my own.

However, the West Hunter is long, so I’m only doing the first year for now:

My friend the Witch Doctor:

Only a handful of Herero shared my skepticism about witchcraft. People in the neighborhood as well as several other employees were concerned about Kozondo’s problem. They told me that he had to be taken to a well known local witch doctor. “Witch doctor” I said, “you all have been watching too many low budget movies. We call them traditional healers these days, not witch doctors”. They all, including Kozondo, would have none of it. “They are bad and very dangerous people, not healers” he said. It quickly became apparent that I was making a fool of myself trying to explain why “traditional healer” was a better way to talk than “witch doctor”. One of our group had some kind of anti-anxiety medicine. We convinced Kozondo to try one but it had no effect at all. Everyone agreed that he must consult the witch doctor so we took him. …

That evening we had something like a seminar with our employees and neighbors about witchcraft. Everyone except the Americans agreed that witchcraft was a terrible problem, that there was danger all around, and that it was vitally important to maintain amicable relations with others and to reject feelings of anger or jealousy in oneself. The way it works is like this: perhaps Greg falls and hurts himself, he knows it must be witchcraft, he discovers that I am seething with jealousy of his facility with words, so it was my witchcraft that made him fall. What is surprising is that I was completely unaware of having witched him so he bears me no ill will. I feel bad about his misfortune and do my best to get rid of my bad feelings because with them I am a danger to friends and family. Among Herero there is no such thing as an accident, there is no such thing as a natural death, witchcraft in some form is behind all of it. Did you have a gastrointestinal upset this morning? Clearly someone slipped some pink potion in the milk. Except for a few atheists there was no disagreement about this. Emotions get projected over vast distances so beware.

Even more interesting to us was the universal understanding that white people were not vulnerable to witchcraft and could neither feel it nor understand it. White people literally lack a crucial sense, or part of the brain. An upside, I was told, was that we did not face the dangers that locals faced. On the other hand our bad feelings could be projected so as good citizens we had to monitor carefully our own “hearts”.

Amish Paradise:

French Canadian researchers have shown that natural selection has noticeably sped up reproduction among the inhabitants of Île aux Coudres, an island in the St. Lawrence River –  in less than 150 years. Between 1799 and 1940, the age at which women had their first child dropped from 26 to 22, and analysis shows this is due to genetic change.

… Today the French of Quebec must  differ significantly (in those genes that influence this trait)  from people in France, which has had relatively slow population growth.  …

The same must be the case for old American types whose ancestors – Puritans, for example – arrived early and went through a number of high-fertility generations in colonial days.  It’s likely the case for the Mormons, who are largely descended from New Englanders. I’ve heard of odd allele frequencies  in CEU  (involving FSH) that may relate to this.

Something similar must be true of the Boers as well.

I would guess that a similar process operated among the first Amerindians that managed to get past  the ice in North America.  America south of the glaciers would have been a piece of cake for anyone tough enough to make a living as a hunter in Beringia – lush beyond belief, animals with no experience of humans.

Six Black Russians:

(Black Russians are, I think, an alcoholic beverage.)

Every now and then, I notice someone, often an anthropologist,  saying that human cognitive capability just has to be the same in all populations.  According to Loring Brace, “Human cognitive capacity , founded on the ability to learn a language, is of equal survival value to all human groups, and consequently there is no valid reason to expect that there should be average differences in intellectual ability among living human populations. ”

There are a lot of ideas and assumptions in that quote, and as far as I can tell, all of them are wrong.  …

Populations vary tremendously in the fraction that contributes original work in science and technology – and that variation mostly agrees with the distribution of IQ.

And Your Little Dog, Too!

As I have mentioned before,  the mtDNA of European hunter-gathers seems to be very different from that of modern Europeans. The ancient European mtDNA pool was about 80% U5b – today that lineage is typically found at 10% frequency or lower, except in northern Scandinavia. Haplogroup H, currently the most common in Europe, has never been found in early Neolithic or  pre-Neolithic Europeans.  …

Interestingly, there is a very similar  pattern in canine mtDNA.  Today Europeans dogs fall into four haplotypes: A (70%), B(16%), C (6%), and D(8%).  But back in the day, it seems that the overwhelming majority of dogs (88%)  were type C,  12% were in group A, while B and D have not been detected at all.

Lewontin’s Argument 

(always bears re-addressing)

Richard Lewontin argued that since most (> 85%) genetic variation in humans is within-group, rather than between groups, human populations can’t be very different. Of course, if this argument is valid, it should apply to any genetically determined trait. Thus the  variation in skin color within a population should be larger than the skin color differences between populations – except that it’s not. The difference in skin color between Europeans and Pygmies is large, so large that there is no overlap at all.

The Indo-European Advantage

There is a large region of homogeneity on European haplotypes with the mutation [for lactose tolerance], telling us that it has arisen to high frequency within the last few thousand years. …

In a dairy culture where fresh milk was readily available, children who could drink it obtained about 40% more calories from milk than children who were not LT.

Consider that 1 Liter of cow’s milk has

* 250 Cal from lactose
* 300 Cal from fat
* 170 Cal from protein

or 720 Calories per liter. But what if one is lactose intolerant? Then no matter whether or not flatulence occurs that person does not get the 250 Calories of lactose from the liter of milk, but only gets 470.

The Hyperborean Age

I was contemplating Conan the Barbarian, and remembered the essay that Robert E. Howard wrote about the  background of those stories – The Hyborian Age.  I think that the flavor of Howard’s pseudo-history is a lot more realistic than the picture of the human past academics preferred over the past few decades. …

Given the chance (sufficient lack of information), American anthropologists assumed that the Mayans were peaceful astronomers. Howard would have assumed that they were just another blood-drenched snake cult: who came closer? …

Most important, Conan, unlike the typical professor, knew what was best in life.

Class, Caste, and Genes: 

If there is any substantial heritability of merit, where merit is whatever leads to class mobility, then mobility ought to turn classes into hereditary castes surprisingly rapidly.

A start at looking into genetic consequences of meritocracy is to create the simplest possible model and follow its implications. Consider free meritocracy in a two class system, meaning that each generation anyone in the lower class who has greater merit than someone in the upper class immediately swaps class with them. …

Back to the book. Chapter 3: Agriculture: The Big Change

This chapter’s thesis is the crux of the book: agriculture simultaneously exposed humans to new selective pressured and allowed the human population to grow, creating a greater quantity of novel mutations for natural selection to work on.

Sixty thousand years ago, before the expansion out of Africa, there were something like a quarter of a million modern humans. By the Bronze Age, 3,000 years ago that number was roughly 60 million. 

Most random mutations fall somewhere between “useless” and “kill you instantly,” but a few, like lactase persistence, are good. I’m just making up numbers, but suppose 1 in 100 people has good, novel mutation. If your group has 100 people in it (per generation), then you get one good mutation. If your group has 1,000 people, then you get 10 good mutations.

Evolution isn’t like getting bitten by a radioactive spider–it can only work on the genetic variation people actually have. More genetic variation=more chances at getting a good gene that helps people survive.

Or to put it another way, we can look at a population and use “time” as one of our dimensions. Imagine a rectangle of people–all of the people in a community, over time–100 people in the first generation, 100 in the second, etc. After enough time, (10 generations or about 200 years,) you will have 1,000 people and of course hit 10 favorable mutations.

Increasing the population per generation simply increases the speed with which you get those 10 good mutations.

Interestingly:

One might think that it would take much longer for a favorable mutation to spread through such a large population than it would for one to spread through a population as small as the one that existed in the Old Stone Ag. But sine the frequency of an advantageous allele increases exponentially with time in a well-mixed population, rather like the flu, it takes only twice as long to spread through a population of 100 million as it does to spread through a population of 10,000.

The authors note that larger populations can generate more good, creative ideas, not just genes.

Agriculture–and its attendant high population densities–brought about massive cultural changes to human life, from the simple fact of sedentism (for non-pastoralists) to the ability to store crops for the winter, build long-term housing, and fund governments, which in turn created and enforced laws which further changed how humans lived and interacted. 

(Note: “government” pre-dates agriculture, but was rather different when people had no surplus grain to take as taxes.)

Agriculture also triggered the spread of plagues, as people now lived in groups large (and often squalid) enough to breed and transmit them. Related: Evidence for the Plague in Neolithic Farmers’ Teeth.

Plagues have been kind of a big deal in the history of civilization.

On government:

Combined with sedentism, these developments eventually led to the birth of governments, which limited local violence. Presumably, governments did this because it let them extract more resources from their subjects…

Peasants fighting among themselves interferes with the economy. Governments don’t like it and will tend to hang the people involved.

Some people call it self-domestication.

Recent studies have found hundreds of ongoing [genetic] sweeps–sweeps begun thousands of years ago that are still in progress today. Some alleles have gone to fixation, more have intermediate frequencies, and most are regional. Many are very recent: the rate of origination peaks at around 5,000 years ago in the European and Chinese samples, and about 8,500 years ago in the African sample.

I assume that these genes originating about 5,000 years ago are mostly capturing the Indo-European (pastoralist) and Anatolian (farming) expansions. I don’t know what happened in China around 5,000 years ago, but I wouldn’t be surprised if whatever triggered the Indo-Europeans to start moving in central Asia were connected with events further to the east.

IIRC, 8,500 years ago is too early for the Bantu expansion in Africa, so must be related to something else.

There is every reason to think that early farmers developed serious health problems from this low-protein, vitamin -short, high-carbohydrate diet. Infant mortality increased, and the poor diet was likely one of the causes. you can see the mismatch between the genes and the environment in the skeletal evidence Humans who adopted agriculture shrank: average height dropped  by almost five inches.

I have seen this claim many times, and still find it incredible. I am still open to the possibility of it having been caused by a third, underlying factor, like “more people surviving diseases that had formerly killed them.”

There are numerous signs of pathology in the bones of early agriculturalists. In the Americas, the introduction of maize led to widespread tooth decay and anemia due to iron deficiency…

Of course, over time, people adapted to their new diets. You are not a hunter-gatherer. (Probably. If you are, hello!)

…Similarly, vitamin D shortages in the new die may have driven the evolution of light skin in Europe and northern Asia. Vitamin D is produced by ultraviolet radiation from the sun acting on our skin… Since there is plenty of vitamin D in fresh meat, hunter-gatherers in Europe may not have suffered from vitamin D shortages and thus may have been able to get by with fairly dark skin. In fact, this must have been the case, since several of the major mutations causing light skin color appear to have originated after the birth of agriculture. vitamin D was not abundant in the new cereal-based diet, and any resulting shortages would have been serious, since they could lead to bone malformations (rickets,) decreased resistance to infectious diseases, and even cancer. …

I have read that of the dark-skinned peoples who have recently moved to Britain, the vegetarians among them have been the hardest-hit by vitamin D deficiency. Meat is protective. 

Peoples who have farmed since shortly after the end of the Ice Age (such as the inhabitants of the Middle East) must have adapted most thoroughly to agriculture. In areas where agriculture is younger, such as Europe or China, we’d expect to see fewer adaptive changes… In groups that had remained foragers, there would presumably be no such adaptive changes…

Populations that have never farmed or that haven’t farmed for long, such as the Australian Aborigines and many Amerindians, have characteristic health problems today when exposed to Western diets.

EG, Type 2 diabetes.

Dr. (of dentistry) Weston Price has an interesting book, Nutrition and Physical Degeneration, that describes people Price met around the world, their dental health, and their relationship to Western or traditional diets. (Written/published back in the 1930s.) I’m a fan of the book; I am not a fan of the kind of weird organization that publishes it. That organization promotes fringe stuff like drinking raw milk, but as far as I can recall, I didn’t see anything about drinking raw milk in the entirety of Dr. Price’s tome; Dr. Price wasn’t pushing anything fringe, but found uncontroversial things like “poverty-stricken children during the Great Depression did better in school when given nutritious lunches.” Price was big on improper nutrition as the cause of tooth decay and was concerned about the effects of industrialization and Western diets on people’s bones and teeth.

So we’ve reached the end of Chapter 3. What did you think? Do you agree with Greg and Henry’s model of how Type 2 Diabetes arises, or with the “thrifty genotype” promulgated by James Neel? And why do metabolic syndromes seem to affect poor whites more than affluent ones?

What about the higher rates of FAS among African Americans than the French (despite the French love of alcohol) or the straight up ban on alcohol in many Islamic (ancient farming) cultures? What’s going on there?

And any other thoughts you want to add.

See you next Wednesday for chapter 4.

Finnis, Saami, and Fennoscandian DNA

 

800px-Lenguas_finougrias
Distribution of the Finno-Ugric languages

I’ve long wondered which group arrived first in Europe: the Indo-Europeans or the Finno-Ugrics. Most Europeans speak one of the hundreds of languages in the Indo-European family tree, but a few groups speak languages from the mostly Siberian Finno-Ugric branch of the Uralic family.

(Sorry, guys, I’m out of practice writing and these sentences don’t sound good to me, but the only way to improve is to forge ahead, so let’s go.)

Major countries/ethnic groups that speak Finno-Ugric languages include the Finns (obviously,) Saami/Lapps, Hungarians, and Estonians. The most southerly of this family, Hungarian, arrived in the Carpathian Basin within the span of recorded History (in 894 or 895, followed by a few years of warfare to secure their territory,) but the origins of the other European Finno-Ugric languages remains mysterious.

Who arrived first, the Indo Europeans or the Finns? Did the Saami always live in their current homelands, or did they once range much further south or east? Did they migrate here recently or long ago (since the entire area was under ice sheets during the ice age, no one lived there tens of thousands of years ago.)

With the exception of Hungarian, these languages all hail from the far north (especially if you include the Samoyidic languages, which hail from north of Komi on the map,) a cold and forbidding land where herding, hunting, gathering, and fishing have remained the primary way of life until quite recently–the long winters making agriculture very difficult.

Lamnidis et al have a new paper out on Ancient Fennoscandian DNA that sheds a fascinating light on the subject:

Here we analyse ancient genomic data from 11 individuals from Finland and north-western Russia. We show that the genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago. This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today. Additionally, we show that ancestors of modern Saami inhabited a larger territory during the Iron Age, which adds to the historical and linguistic information about the population history of Finland.

41467_2018_7483_fig1_htmlLet’s cut to the pictures, because they are worth a thousand words:

Just in case you are unclear on the geography, the Modern Saami come from northern part of the Finnoscandian peninsula. Six of the ancient remains came from Bolshoy Oleni Ostrov in the Murmansk Region on the Kola Peninsula–that’s the topmost dot on the map, now in Russia. These remains are very old–dated to about 1610-1436 BC.

Seven remains came from Levänluhta in Isokyrö, Finland, from a more recent burial dated to around 300-800 AD. (Actually, I think Levanluhta is a lake, so  This is the most southwestern burial on the map, in an area where the modern Finns live.

And the remains of two people came from a much more recent Saami cemetery in the Kola peninsula, Chalmny Varre, dating from the 17 or 1800s.

All of this DNA was compared against a variety of reference populations:

41467_2018_7483_fig2_html

(I would just like to pause for a moment to appreciate both the beauty and hard work that went into these graphs.)

PC2 graphs are a little complicated, but what we’re basically looking at (in color) are two different human population axes. They very roughly correlate to north-south (up and down) and east-west, (left to right), because people tend to be more closely related to their neighbors than people thousands of miles away, but there’s another, more fascinating story going on here.

On the right-hand side, we have a cline that maps very nicely to north and south, from the Yukagir–a people from a part of Russia that’s so far to the northeast it’s almost in Alaska–at the top and the Semende of Indonesia and the Atayal, an indigenous Taiwanese group, at the bottom. (Most Taiwanese you meet are either newly arrived Han Chinese or older Han Chinese; the aboriginal Taiwanese are different, but likely the ancestors of Polynesians.)

AsianDNA1
DNA from various Asian peoples

Most east Asian DNA shows up as a blend of these two groups (which we may call roughly polar and tropical). In the chart to the right, taken from Haak et al, the polar DNA is red and the tropical is yellow. So the up-down cline on the right side of the map represents which particular mix of Polar/Tropical DNA these folks have.

On the left side of the graph, we have a farming/hunter-gatherer cline. The first farmers hailed from Anatolia (now Turkey, but that was before the Turks moved to Turkey,) and subsequently spread/conquered most of Europe and probably a few other places, because agriculture was quite successful. So the orange is Middle Easterners; above them are southern Europeans like Albanians and Basques; then the English, French, Hungarians, Finns, etc; and finally some older burials of people with descriptive names like “Eastern Hunter-Gatherer” [EHG] or “Scandinavian Hunter-gatherers” [SHG].

(I have to constantly remind myself what these little abbreviations mean, but The Genetic Prehistory of the Baltic Region probably clears things up a bit:

Similarly, in the Eastern Baltic, where foraging continued to be the main form of subsistence until at least 4000 calBCE15, ceramics technology was adopted before agriculture, as seen in the Narva Culture and Combed Ceramic Culture (CCC). Recent genome-wide data of Baltic pottery-producing hunter-gatherers revealed genetic continuity with the preceding Mesolithic inhabitants of the same region as well as influence from the more northern EHG21,22, but did not reveal conclusively whether there was a temporal, geographical or cultural correlation with the affinity to either WHG or EHG.

The transition from the Late (Final) Neolithic to the Early Bronze Age (LNBA) is seen as a major transformative period in European prehistory, accompanied by changes in burial customs, technology and mode of subsistence as well as the creation of new cross-continental networks of contact seen in the emergence of the pan-European Corded Ware Complex (CWC, ca. 2900–2300 calBCE) in Central2 and north-eastern Europe21.

If you remember your Guns, Germs, and Steel, Turkish farmers had a really hard time getting their wheat to grow up in really cold places like Northern Russia,  Scandinavia and Narva (near the border between Estonia and Russia on the Baltic Sea,) which is why modern Finland is super poor and Turkey and Mexico, where corn was domesticated, are rich–what it doesn’t quite work like that?

Okay.

Anyway.

So most Europeans today are a mix of Anatolian farmers and various European hunter gatherer groups, with exactly how much you got depending a lot on whether the local environment was hospitable to farming. The pure hunter-gatherer genomes therefore show up as “further north” than the mixed, modern genomes of modern French and British folks.

There were additional events besides the Anatolian conquest that shaped modern European genetics–mostly the aforementioned Indo-European conquest–but the Indo-Europeans were at least part hunter-gatherer by DNA (nomadic pastoralists by profession,) so on this scale, their contributions look a lot like the older hunter-gatherer DNA.

So the interesting part of the graph is the middle, where all of the central Eurasian peoples are plotted. The purple band is various Finno-Ugric/Uralic speakers.

Hungarians are solidly in Europe because the ancient conquering Magyars left behind their language, but not much of their DNA (as we’ve discussed previously.) The Nganasan are one of the most thoroughly Siberian peoples you can imagine; they historically survived by hunting reindeer.

The green swaths (light and dark teal) are mostly Turkic-language speaking peoples; the Turkic peoples originated near Mongolia/Korea and spread out from there, mostly absorbing the DNA of whomever they encountered and passing on their language. The authors have also included Mongolian (which is not in the Turkic language family) in the light green group and some Caucuses groups in the dark teal.

Interestingly, the Yukaghir language (far upper right) is (according to Wikipedia,) potentially in the greater Finno-Ugric/Uralic family:

The relationship of the Yukaghir languages with other language families is uncertain, though it has been suggested that they are distantly related to the Uralic languages, thus forming the putative Uralic–Yukaghir language family.[5]

Based on the genetics, I’d say it looks very likely that the ancestors of Uralic-speaking Nganasan and the Yukagirs were conversing in some sort of mutually intelligible language. Unfortunately, Yukaghir has very few speakers and is likely to die, so there’s not much time to research it.

Finally in the Light Teal we have some groups from Pakistan/Afghanistan, like the Balochi.

(Note that all of the colors used in these studies are arbitrary; DNA doesn’t really have a color.)

So where do our ancient DNA remains fall on this graph?

Today, the Levanluhta site is in Finland, surrounded solidly by Finns (and maybe some random Scandinavians; who knows;) in 300-800 AD, the population was almost identical to modern Saami. So even though Saami and Finns both speak Finno-Ugric languages, the Finns replaces the Saami in this area sometime in the past 1,500 years or so.

One Levanlughta skeleton is an exception–the one marked Levanlughta_B; it is clearly closer to the Finns and English on this graph, but deeper mathematical analysis disputes this conclusion:

One of the individuals from Levänluhta (JK2065/Levänluhta_B) rejects a cladal position with modern Saami to the exclusion of most modern Eurasian populations. This individual also rejects a cladal position with Finns. We analysed low coverage genomes from four additional individuals of the Levänluhta site using PCA (Supplementary Figure 3), confirming the exclusive position of Levänluhta_B compared to all other six individuals (including the four low-coverage individuals) from that site, as is consistent with the ADMIXTURE and qpAdm results. The outlier position of this individual cannot be explained by modern contamination, since it passed several tests for authentication (see Methods) along with all other ancient individuals. However, no direct dating was available for the Levänluhta material, and we cannot exclude the possibility of a temporal gap between this individual and the other individuals from that site.

In other words, it is a mystery.

The remains from Chalmny Varre, which we know was a Saami cemetery, unsurprisingly cluster with the other Saami.

The Bolshoy remains, though, are quite interesting. They are shifted slightly in the direction of the ancient hunter-gatherers (perhaps their descendants, if still around, have mixed a bit with the agriculturalists.) Their physical location is about as far east as the Red Squares (ethnic Russians,) yet the more closely resemble the Mansi or the Selkups. (The modern Mansi live here; the modern Selkups live nearby.)

Getting down to the bar graphs, we see this data presented in a different way.

There are three groups that we can see contributing to most modern Europeans–Farmers, represented by the Orange LBK DNA; exclusively Indo-European, Green, notably not found in the Basque; and hunter-gatherers in Dark Blue. (Note that the ancestors of the Indo-Europeans hailed from the Central Eurasian steppes and so their DNA could have gotten around there, too.)

The modern Saami also have a Purple component to their DNA, which finds its highest expression in the Nganasan of far eastern polar Russia.

So the oldest burials–the Bolshoy–show no agricultural DNA. They are hunter-gatherers+Siberians, with a touch of Indo-European (probably from a steppe population that might have contributed to the Indos as well) and a bit they share with… the Karitiana of Brazil? Well, the Native Americans did descend from Paleo Siberians, so some genetic relatedness is expected.

The more recent burials, which cluster with the modern Saami, all show agricultural DNA–probably due to marrying a few of the local Finns/Russians who carry some agricultural DNA (who are almost genetically identical on this scale) rather than a pure LBK agriculturalist.

Here we see why the one outlier, Levanlughta_B, doens’t group with the Finns, either–modern Finns and Russians have some of that Nganasan-style Siberian DNA (probably from the same process that gifted Finnish/Russian DNA to the Saami), but Levanlughta_B doesn’t. Levanlughta_B looks more like the Baltic BA sample (Baltic Bronze Age.) Perhaps this individual was just a merchant, traveler, or lost–or represents a stage before the modern Finnish population had been produced.

The Finnish population itself is interesting, because it is genetically very similar to the Russian, but obviously speaks a language far more closely related to Saami (Lapp) than anything in the Indo-European tree. While it is therefore likely that the Finns replaced the Saami in the area around Lake Levanlughta, it seems also probable that in the process, they absorbed a large number of Uralic-speaking people. Who conquered (or married) whom? Did an ancient Balto-Slavic population move into what is now Finland, marry the local Saami girls, and adopt their language? Did an ancient Siberian population speaking a Uralic language conquer some ancient group of Russians, take their women, pass on their Uralic language, and later move into Finland and drive out the locals? Or perhaps something even more complicated occurred.

As for the Bolshoy, are they related (closely) to the modern Saami, or are they a group that simply died out?

The paper goes on:

 While the Siberian genetic component presented here [Purple] has been previously described in modern-day populations from the region1,3,9,10, we gain further insights into its temporal depth. Our data suggest that this fourth genetic component found in modern-day north-eastern Europeans arrived in the area before 3500 yBP. It was introduced in the population ancestral to Bolshoy Oleni Ostrov individuals 4000 years ago at latest, as illustrated by ALDER dating using the ancient genome-wide data from the Bolshoy samples. The upper bound for the introduction of this component is harder to estimate. The component is absent in the Karelian hunter-gatherers (EHG)3 dated to 8300–7200 yBP as well as Mesolithic and Neolithic populations from the Baltics from 8300 yBP and 7100–5000 yBP respectively8

Karelia is a region that crosses the border between Finland and Russia, so it is significant that this Siberian component isn’t found in ancient Karelian hunter-gatherers. Of course, the Siberians could have just been further north, however, the authors note that we have archaeological evidence of the spread of the Bolshoy people:

The large Nganasan-related component in the Bolshoy individuals from the Kola Peninsula provides the earliest direct genetic evidence for an eastern migration into this region. Such contact is well documented in archaeology, with the introduction of asbestos-mixed Lovozero ceramics during the second millennium BC50, and the spread of even-based arrowheads in Lapland from 1900 BCE51,52. Additionally, the nearest counterparts of Vardøy ceramics, appearing in the area around 1,600-1,300 BCE, can be found on the Taymyr peninsula, much further to the East51,52. Finally, the Imiyakhtakhskaya culture from Yakutia spread to the Kola Peninsula during the same period24,53. Contacts between Siberia and Europe are also recognised in linguistics. The fact that the Nganasan-related genetic component is consistently shared among Uralic-speaking populations, with the exceptions of absence in Hungarians and presence in the non-Uralic speaking Russians, makes it tempting to equate this genetic component with the spread of Uralic languages in the area.

The authors qualify this with a bit of “it’s complicated; people move around a lot,” but basically it’s People: not pots.

That was an enjoyable read; I look forward to the next paper from these folks.

Book Club: The 10,000 Year Explosion pt. 2: Behavioral Modernity 

 

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Neanderthal skull

Welcome back to EvX’s book club. Today we’re discussing Cochran and Harpending’s The 10,000 Year Explosion: How Civilization Accelerated Human Evolution, chapter 2: The Neanderthal Within.

How did you like the chapter?

Unless I have missed a paper somewhere, this is a remarkable chapter, for The 10,000 Year Explosion was published in 2009, and the first Neanderthal genome showing more overlap with Europeans (and Asians) than Sub-Saharans was published in 2010. Greg and Henry did know of genetic evidence that humans have about 5% admixture from some archaic sister-species, but no one yet had evidence of which species, nor was there popular agreement on the subject. Many scientists still rejected the notion of Sapiens-Neanderthal interbreeding when Cochran and Harpending laid out their bold claim that not only had it happened, but it was a critical moment in human history, jump-starting the cultural cultural effervescence known as behavioral modernity.

Homo sapiens have been around for 300,000 years–give or take a hundred thousand–but for most of that time, we left behind rather few interesting artifacts. As the authors point out, we failed to develop agriculture during the Eemian interglacial (though we managed to develop agriculture at least 7 times, independently, during the current interglacial). Homo sapiens attempted to leave Africa several times before 70,000 years ago, but failed each time, either because they weren’t clever enough to survive in their new environment or couldn’t compete with existing hominins (ie, Neanderthals) in the area.

DBoAOVxWsAAYu6jSapiens’ technology didn’t do much interesting for the first couple hundred thousand years, either. Yet 70,000 years ago, sapiens did manage to leave Africa, displace the Neanderthals, spread into radically new climates, developed long distance trade and art, and eventually agriculture and everything we now enjoy here in the modern world.

According to Wikipedia, behavioral modernity includes:

Burial, fishing, art, self-decoration via jewelry or pigment, bone tools, sharp blades, hearths, multi-part tools, long-distance transportation of important items, and regionally distinct artifacts.

This leaves two important questions re: Cochran and Harpending’s theory. First, when exactly did behavioral modernity emerge, and second, was it a gradual transition or a sudden explosion?

Prehistoric art is tricky to date–and obviously did not always get preserved–but Blombos Cave, South Africa, currently contains our earliest piece, from about 70,000-100,000 years ago. The Blombos art is not figurative–it’s patterns of crosshatched lines–but there’s a fair amount of it. Blombos appears to have been an ochre-processing spot (the art is made with or on pieces of ochre) littered with thousands of leftover scraps. According to Wikipedia:

In 2008 an ochre processing workshop consisting of two toolkits was uncovered in the 100,000-year-old levels at Blombos Cave, South Africa.[3] Analysis shows that a liquefied pigment-rich mixture was produced and stored in the shells of two Haliotis midae (abalone), and that ochre, bone, charcoal, grindstones and hammer-stones also formed a composite part of the toolkits. As both toolkits were left in situ, and as there are few other archaeological remains in the same layer, it seems the site was used primarily as a workshop and was abandoned shortly after the pigment-rich compounds were made. Dune sand then blew into the cave from the outside, encapsulated the toolkits and by happenstance ensured their preservation before the next occupants arrived, possibly several decades or centuries later.

The application or use of the compound is not self-evident. No resins or wax were detected that might indicate it was an adhesive for hafting.

70 beads made from shells with holes drilled in them have also been found at Blombos.

Blombos is interesting, but the “art” is not actually very good–and we can’t say for sure that it was meant as art at all. Maybe the locals were just scraping the rocks to get the ochre off, for whatever purposes.

Indisputable art emerges a little later, around 40,000 years ago–simultaneously, it appears, in Europe, Asia, Australia, and Indonesia. The archaeology of Africa is less well-documented (in part because things just disintegrate quickly in some areas), but the earliest known sub-Saharan figurative art is about 26,000 years old. This art is both more advanced (it actually looks like art) and more abundant than its predecessors–the Sungir burial, dated to around 30,000-34,000 BC, for example, contains over 13,000 beads–a stark contrast to Blombos’s 70.

722px-homo_sapiens_lineage-svgIf a specific event triggered the simultaneous development of figurative art–and other aspects of behavioral modernity–in four different parts of the world, that event would logically have occurred before those groups split up. The timing of our interbreeding with Neanderthals–“In Eurasia, interbreeding between Neanderthals and Denisovans  with modern humans took place several times between about 100,000 and 40,000 years ago, both before and after the recent out-of-Africa migration 70,000 years ago”–is therefore temporaly perfect.

Subsequent back-migration could have then carried the relevant Neanderthal genomes into Africa–for regardless of where or how behavioral modernity started, all humans now have it.

So what do you think? Did we talk the Neanderthals to death? Did we get the gene for talking from the Neanderthals? Did we out-think them? Or did we just carry some disease or parasite that wiped them out? Or did they wipe themselves out via maternal death in labor, due to their enormous skulls?

(As for FOXP2, it appears that the version found in humans and Neanderthals is slightly different, so I find it a little doubtful that we got it from them.)

A couple of interesting quotes:

In several places, most clearly in central and southwestern France and part of northern Spain, we find a tool tradition that lasted from about 35,000 to 28,000 years ago (the Chatelperronian) that appears to combine some of the techniques of the Neanderthals … with those of modern humans. … Most important, there are several skeletons clearly associated with the Chatelperronian industry, and all are Neanderthal. This strongly suggests that there were interactions between the populations, enough that the Neanderthals learned some useful techniques from modern humans.

The smoking gene?

P. D. Evans and his colleagues at the University of Chicago looked at microcephalin (MCPH1), a very unusual gene that regulates brain size. They found that most people today carry a version that is quite uniform, suggesting that it originated recently. At the same time, it is very different from other, more varied versions found  at the same locus in humans today, all of which have many single-nucleotide differences among them. More than that, when there are several different versions of a gene at some locus, we normally find some intermediate versions created by recombination, that is, by chromosomes occasionally breaking and recombining. In the case of the unusual gene (called D for “derived”) at the microcephalin locus, such recombinants are very rare: It is as if the common, highly uniform version of microcephalin simply hasn’t been in the human race all that long in spite of the high frequency of the new version in many human populations. The researchers estimated that it appeared about 37,000 years ago (plus or minus a few tens of thousands of years.) And if it did show up then, Neanderthals are a reasonable, indeed likely, source.

So far as I know (and I looked it up a few weeks ago) no one has yet found microcephalin D in Neanderthals–and the date of 37,000 years ago sounds a bit too recent. However, we haven’t actually genotyped that many Neanderthals (it’s hard to find good 40,000 year old DNA), so we might just not have found it yet–and the date might simply be wrong.

It’s a remarkable genetic finding, even if it didn’t involve Neanderthals–and it might be simpler to dispense with other standards and define Homo sapiens as starting at this point.

On a related note, here’s a bit from Wikipedia about the ASPM gene:

A new allele (version) of ASPM appeared sometime between 14,100 and 500 years ago with a mean estimate of 5,800 years ago. The new allele has a frequency of about 50% in populations of the Middle East and Europe, it is less frequent in East Asia, and has low frequencies among Sub-Saharan African populations.[12] It is also found with an unusually high percentage among the people of Papua New Guinea, with a 59.4% occurrence.[13]

The mean estimated age of the ASPM allele of 5,800 years ago, roughly correlates with the development of written language, spread of agriculture and development of cities.[14] Currently, two alleles of this gene exist: the older (pre-5,800 years ago) and the newer (post-5,800 years ago). About 10% of humans have two copies of the new ASPM allele, while about 50% have two copies of the old allele. The other 40% of humans have one copy of each. Of those with an instance of the new allele, 50% of them are an identical copy.[15] The allele affects genotype over a large (62 kbp) region, a so called selective sweep which signals a rapid spread of a mutation (such as the new ASPM) through the population; this indicates that the mutation is somehow advantageous to the individual.[13][16]

Testing the IQ of those with and without new ASPM allele has shown no difference in average IQ, providing no evidence to support the notion that the gene increases intelligence.[16][17][18] However statistical analysis has shown that the older forms of the gene are found more heavily in populations that speak tonal languages like Chinese or many Sub-Saharan African languages.[19]

We still have so much to discover.

Book Club: The 10,000 Year Explosion pt 1

 

5172bf1dp2bnl-_sx323_bo1204203200_For most of he last century, the received wisdom in the social sciences has been that human evolution stopped a long time ago–in the most up-to-date version, before modern humans expanded out of Africa some 50,000 years ago. This implies that human minds must be the same everywhere–the “psychic unity of mankind.” It would certainly make life simpler if it were true.

Thus Cochran and Harpending fire the opening salvo of  The 10,000 Year Explosion: how Civilization Accelerated Human Evolution. (If you haven’t finished the book yet, don’t worry–we’ll discuss one chapter a week, so you have plenty of time.)

The book’s main thesis–as you can guess by reading the title–is that human evolution did not halt back in the stone age, but has accelerated since then.

I’ve been reading Greg and Henry’s blog for years (now Greg’s blog, since Henry sadly passed away.) If you’re a fan of the blog, you’ll like the book, but if you follow all of the latest human genetics religiously, you might find the book a bit redundant. Still, it is nice to have many threads tied together in one place–and in Greg & Henry’s entertaining style. (I am about halfway through the book as of this post, and so far, it has held up extremely well over the years since it was published.)

Chapter One: Conventional Wisdom explains some of the background science and history necessary to understand the book. Don’t worry, it’s not complicated (though it probably helps if you’ve seen this before.)

A lot of of our work could be called “genetic history.” … This means that when a state hires foreign mercenaries, we are interested in their numbers, their geographic origin, and the extent to which they settled down and mixed with the local population. We don’t much care whether they won their battles, as long as they survived and bred. …

For an anthropologist it might be important to look at how farmers in a certain region and time period lived; for us, as genetic historians, the interesting thing is how natural selection allowed agriculture to come about to begin with, and how the pressures of an agricultural lifestyle allowed changes in the population’s genetic makeup to take root and spread.

One of the things I find fascinating about humans is that the agricultural revolution happened more or less independently in 11 different places, all around 10,000 years ago. There’s a little variation due to local conditions and we can’t be positive that the Indus Valley didn’t have some influence on Mesopotamia and vice versa, but this is a remarkable convergence. Homo sapiens are estimated to have been around for about 200-300,000 years, (and we were predated by a couple million years of other human ancestor-species like Homo erectus)  but for the first 280,000 years or so of our existence no one bothered to invent agriculture. Then in the span of a few thousand years, suddenly it popped up all over the darn place, even in peoples like the Native Americans who were completely isolated from developments over in Asia and Africa.

This suggests to me that some process was going on simultaneously in all of these human populations–a process that probably began back when these groups were united and then progressed at about the same speed, culminating in the adoption of agriculture.

One possibility is simply that humans were hunting the local large game, and about 10,000 years ago, they started running out. An unfortunate climactic event could have pushed people over the edge, reducing them from eating large, meaty animals to scrounging for grass and tubers.

Another possibility is that human migrations–particularly the Out of Africa Event, but even internal African migrations could be sufficient–caused people to become smarter as they encountered new environments, which allowed them to make the cognitive leap from merely gathering food to tending food.

A third possibility, which we will discuss in depth next week, is that interbreeding with Neanderthals and other archaic species introduced new cognitive features to humanity.

And a fourth, related possibility is that humans, for some reason, suddenly developed language and thus the ability to form larger, more complex societies with a division of labor, trade, communication, and eventually agriculture and civilization.

We don’t really know when language evolved, since the process left behind neither bones nor artifacts, but if it happened suddenly (rather than gradually) and within the past 300,000 years or so, I would mark this as the moment Homo sapiens evolved.

While many animals can understand a fair amount of language (dogs, for instance) and some can even speak (parrots,) the full linguistic range of even the most intelligent apes and parrots is still only comparable to a human toddler. The difference between human language abilities and all other animals is stark.

There is great physical variation in modern humans, from Pygmies to Danes, yet we can all talk–even deaf people who have never been taught sign language seek to communicate and invent their own sign language more complex and extensive than that of the most highly trained chimps. Yet if I encountered a group of “humans” that looked just like some of us but fundamentally could not talk, could not communicate or understand language any more than Kanzi the Bonobo, I could not count them members of my species. Language is fundamental.

But just because we can all speak, that does not mean we are all identical in other mental ways–as you well know if you have ever encountered someone who is inexplicably wrong about EVERYTHING here on the internet.

But back to the book:

We intend to make the case that human evolution has accelerated int he past 10,000 years, rather than slowing or stopping, and is now happening about 100 times faster than its long term average over the 6 million years of our existence.

A tall order!

220px-San_tribesman
Some anthropologists refer to Bushmen as “gracile,” which means they are a little shorter than average Europeans and not stockily built

To summarize Cochran and Harpending’s argument: Evolution is static when a species has already achieved a locally-optimal fit with its environment, and the environment is fairly static.

Human environments, however, have not been static for the past 70,000 years or so–they have changed radically. Humans moved from the equator to the polar circle, scattered across deserts and Polynesian islands, adapting to changes in light, temperature, disease, and food along the way.

The authors make a fascinating observation about hunting strategies and body types:

…when humans hunted big game 100,000 years ago, they relied on close-in attacks with thrusting spears. Such attacks were highly dangerous and physically taxing, so in those days, hunters had to be heavily muscled and have thick bones. That kind of body had its disadvantages–if nothing else, it required more food–but on the whole, it was the best solution in that situation. … but new weapons like the atlatl (a spearthrower) and the bow effectively stored muscle-generated energy, which meant that hunters could kill big game without big biceps and robust skeletons. Once that happened, lightly built people, who were better runners and did not need as much food, became competitively superior. The Bushmen of southern Africa…are a small, tough, lean people, less than five feet tall. It seems likely that the tools made the man–the bow begat the Bushmen.

Cro-magnons (now called “European Early Modern Humans” by people who can’t stand a good name,) were of course quite robust, much more so than the gracile Bushmen (Aka San.) Cro-magnons were not unique in their robustness–in fact all of our early human ancestors seem to have been fairly robust, including the species we descended from, such as Homo heidelbergensis and Homo ergaster. (The debate surrounding where the exact lines between human species should be drawn is long and there are no definite answers because we don’t have enough bones.)

We moderns–all of us, not just the Bushmen–significantly less robust than our ancestors. Quoting from a review of Manthropology: The Science of the Inadequate Modern Male:

Twenty thousand years ago six male Australian Aborigines chasing prey left footprints in a muddy lake shore that became fossilized. Analysis of the footprints shows one of them was running at 37 kph (23 mph), only 5 kph slower than Usain Bolt was traveling at when he ran the 100 meters in world record time of 9.69 seconds in Beijing last year. But Bolt had been the recipient of modern training, and had the benefits of spiked running shoes and a rubberized track, whereas the Aboriginal man was running barefoot in soft mud. …

McAllister also presents as evidence of his thesis photographs taken by a German anthropologist early in the twentieth century. The photographs showed Tutsi initiation ceremonies in which young men had to jump their own height in order to be accepted as men. Some of them jumped as high as 2.52 meters, which is higher than the current world record of 2.45 meters. …

Other examples in the book are rowers of the massive trireme warships in ancient Athens who far exceeded the capabilities of modern rowers, Roman soldiers who completed the equivalent of one and a half marathons a day, carrying equipment weighing half their body weight …

McAllister attributes the decline to the more sedentary lifestyle humans have lived since the industrial revolution, which has made modern people less robust than before since machines do so much of the work. …

According to McAllister humans have lost 40 percent of the shafts of the long bones because they are no longer subjected to the kind of muscular loads that were normal before the industrial revolution. Even our elite athletes are not exposed to anywhere near the challenges and loads that were part of everyday life for pre-industrial people.

Long story short: humans are still evolving. We are not static; our bodies do not look like they did 100,000 years ago, 50,000 years ago, nor even 1,000 years ago. The idea that humans could not have undergone significant evolution in 50–100,000 years is simply wrong–dogs evolved from wolves in a shorter time.

Dogs are an interesting case, for despite their wide variety of physical forms, from Chihuahuas to Great Danes, from pugs to huskies, we class them all as dogs because they all behave as dogs. Dogs can interbreed with with wolves and coyotes (and wolves and coyotes with each other,) and huskies look much more like wolves than like beagles, but they still behave like dogs.

The typical border collie can learn a new command after 5 repetitions and responds correctly 95% of the time, whereas a basset hound takes 80-100 repetitions to achieve a 25 percent accuracy rate.

I understand why border collies are smart, but why are bassets so stupid?

Henry and Greg’s main argument depends on two basic facts: First, the speed of evolution–does evolution work fast enough to have caused any significant changes in human populations since we left Africa?

How fast evolution works depends on the pressure, of course. If everyone over 5 feet tall died tomorrow, the next generation of humans would be much shorter than the current one–and so would their children.

The end of the Ice Age also brought about a global rise in sea level. … As the waters rose, some mountains became islands.. These islands were too small to sustain populations of large predators, and in their absence the payoff for being huge disappeared. … Over a mere 5,000 years, elephants shrank dramatically, from an original height of 12 feet to as little as 3 feet.  It is worth noting that elephant generations are roughly twenty years long, similar to those of humans.

We have, in fact, many cases of evolution happening over a relatively short period, from dogs to corn to human skin tone.

No one is arguing about the evolution of something major, like a new limb or an extra spleen–just the sorts of small changes to the genome that can have big effects, like the minor genetic differences that spell the difference between a wolf and a poodle.

Second, human populations need to be sufficiently distinct–that is, isolated–for traits to be meaningfully different in different places. Of course, we can see that people look different in different places. This alone is enough to prove the point–people in Japan have been sufficiently isolated from people in Iceland that genetic changes affecting appearance haven’t spread from one population to the other.

What about the claim that “There’s more variation within races than between them”?

This is an interesting, non-intuitive claim. It is true–but it is also true for humans and chimps, dogs and wolves. That is, there is more variation within humans than between humans and chimps–a clue that this factoid may not be very meaningful.

Let’s let the authors explain:

Approximately 85 percent of human genetic variation is within-group rather than between groups, while 15 percent is between groups. … genetic variation is distributed in a similar way in dogs: 70 percent of genetic variation is within-breed, while 30 percent is between-breed. …

Information about the distribution of genetic variation tells you essentially nothing about the size or significance of trait differences. The actual differences we observe in height, weight, strength, speed, skin color, and so on are real: it is not possible to argue them away. …

It turns out that the correlations between these genetic differences matter. … consider malaria resistance in northern Europeans and central Africans. Someone from Nigeria may ave the sickle-cell mutation (a known defense against falciparum malaria,) while hardly anyone from northern Europe does, but even the majority of Nigerians who don’t carry the sickle cell are far more resistant to malaria than any Swede. They have malaria-defense versions of many genes. That is the typical pattern you get from natural selection–correlated changes in a population, change in the same general direction, all a response to the same selection pressure.

In other words: suppose a population splits and goes in two different directions. Population A encounters no malaria, and so develops no malria-resistant genes. Population B encounters malaria and quickly develops a hundred different mutations that all resist malaria. If some members of Population B have the at least some of the null variations found in Population A, then there’s very little variation between Pop A and B–all of Pop A’s variants are in fact found in Pop B. Meanwhile, there’s a great deal of variation within Pop B, which has developed 100 different ways to resist malaria. Yet the genetic differences between those populations is very important, especially if you’re in an area with malaria.

What if the differences between groups is just genetic drift?

Most or all of the alleles that are responsible for obvious differences in appearance between populations–such as the gene variants causing light skin color or blue eyes–have undergone strong selection. In these cases, a “big effect” on fitness means anything from a 2 or 3 percent increase on up. Judging from the rate at which new alleles have increased in frequency, this must be the case for genes that determine skin color (SLC24A5), eye color (HERC2), lactose tolerance (LCT), and dry earwax (ABCC11), of all things.

maps-europelighteyesIn fact, modern phenotypes are surprisingly young–blond hair, white skin, and blue eyes all evolved around a mere 10,000 years ago–maybe less. For these traits to have spread as far as they have, so quickly, they either confer some important evolutionary benefit or happen to occur in people who have some other evolutionarily useful trait, like lactose tolerance:

Lactose-tolerant Europeans carry a particular mutation that is only a few thousand years old, and so those Europeans also carry much of the original haplotype. In fact, the shared haplotype around that mutation is over 1 million bases long.

Recent studies have found hundreds of cases of long haplotypeles indicating recent selection: some have reached 100 percent frequency, more have intermediate frequencies, and most are regional. Many are very recent: The rate of origination peaks at around 5,500 years ago in the European and Chinese samples, and at about 8,500 years ago in the African sample.

(Note that the map of blue eyes and the map of lactose tolerance do not exactly correlate–the Baltic is a blue eyes hotspot, but not particularly a lactose hotspot–perhaps because hunter-gatherers hung on longer here by exploiting rich fishing spots.)

Could these explosions at a particular date be the genetic signatures of large conquering events? 5,5000 years ago is about right for the Indo-European expansion (perhaps some similar expansion happened in the East at the same time.) 8,000 years ago seems too early to have contributed to the Bantu Expansion–did someone else conquer west Africa around 8,500 years ago?

Let’s finish up:

Since we have sequenced the chimpanzee genome, we know the size of the genetic difference between chimps and humans. Since we also have decent estimates of the length of time since the two species split, we know the long-term rate of genetic change. The rate of change over the past few thousand years is far greater than this long-term rate over the past few million years, on the order of 100 times greater. …

The ultimate cause of this accelerated evolution was the set of genetic changes that led to an increased ability to innovate. …

Every major innovation led to new selective pressures, which led to more evolutionary change, and the most spectacular of those innovations was the development of agriculture.

Innovation itself has increased dramatically. The Stone Age lasted roughly 3.4 million years (you’ll probably note that this is longer than Homo sapiens has been around.) The most primitive stone tradition, the Oldowan, lasted for nearly 3 million of those 3.4; the next period, the Acheulean, lasted for about 1.5 million years. (There is some overlap in tool traditions.) By contrast, the age of metals–bronze, copper, iron, etc–has been going on for a measly 5,500 years, modern industrial society is only a couple of centuries old–at most.

What triggered this shift from 3 million years of shitty stone tools with nary an innovation in sight to a society that split the atom and put a man on the moon? And once culture was in place, what traits did it select–and what traits are we selecting for right now?

Is the singularity yet to come, or did we hit it 10,000 years ago–or before?

 

By the way, if you haven’t started the book yet, I encourage you to go ahead–you’ve plenty of time before next week to catch up.