Links Post

I have too many open tabs so let’s have a quick “what I’m reading” post

Millenials rediscover concepts like “dorms,” “boarding houses” and “apartments.” I’m not sure how this is novel.

Despite San Jose’s reputation for inclusivity (about 40 percent of residents are foreign born) and economic mobility (ranked best among U.S. cities), Mayor Sam Liccardo says the region’s affordable housing shortage has forced thousands to crash on couches, live in their cars, or stay on the streets.

Here, I think I see your problem:

Despite Because of San Jose’s reputation for inclusivity (about 40 percent of residents are foreign born) and economic mobility (ranked best among U.S. cities), Mayor Sam Liccardo says the region’s affordable housing shortage has forced thousands to crash on couches, live in their cars, or stay on the streets.

There. Fixed it for you.

On the other hand, these startups might be nice places to live.

Greater male variability, this time in response to solar cycles:

The authors use the vital statistics of 320,247 Maine citizens over a 29-year period to show that those born in 3-year peaks of 11-year solar cycles live an average of 1.5 years (CL 1.3–1.7) less than those born in non-peak years. Males are more sensitive than females to this phenomenon, which is statistically demonstrable well into adult life, showing the effect of probable UVR on the early human embryo despite superimposed adult lifetime hazards.

Genetic analysis of social-class mobility in five longitudinal studies:

… we studied social mobility in five cohorts from three countries. We found that people with more education-linked genetics were more successful compared with parents and siblings. We also found mothers’ education-linked genetics predicted their children’s attainment over and above the children’s own genetics, indicating an environmentally mediated genetic effect. Findings reject pure social-transmission explanations of education GWAS discoveries. Instead, genetics influences attainment directly through social mobility and indirectly through family environments.

Interesting Twitter thread on some recent antifa thing: 

White Woman: Your parents would be embarrassed by you–and your grandparents–who have been oppressed by white men throughout history. You should be ashamed of yourself.

Asian Man: Why?

White Woman: Because you’re an Asian giving in to white supremacy, motherfucker

I don’t know anything about Andy Ngo, the photographer who captured this segment and wrote the thread, but I do think there’s some seriously non-self-aware irony in a white person insulting and verbally abusing an Asian person for a perceived failure to feel oppressed by other white people. If she’s so concerned about whites oppressing Asians, maybe she should… stop doing it herself?

Portland is apparently turning into some kind of shithole:

As the crowd made their way to a nearby courthouse, they marched in the middle of the street, bringing traffic to a stop though they didn’t have a permit. Kent Houser, 74, made the mistake of attempting to pass them in his sedan. His car slowly pushed against a masked marcher. The crowd surrounded the car and started kicking it. After speeding down the block, Mr. Houser stepped out and was assaulted by the mob. They pushed him and smashed his car with clubs after he managed to get back inside the vehicle. No police were in sight even though the central precinct was blocks away. …

The mob later occupied a busy intersection. When a middle-aged man driving a car with North Carolina plates stopped in confusion, the agitators descended on him. “You white little f—er!” shouted one white man. “You are a little white supremacist. Go back to North Carolina where you came from.” The driver phoned police for assistance. Nobody came. …

A block away, police officers looked on passively. Why didn’t they respond? The department told me in a statement that it feared intervention would “change the demeanor of the crowd for the worse.”

Such lawlessness is increasingly typical here. Portland’s Resistance organized a protest after Election Day 2016 that turned into a riot. Masked vandals smashed stores and set fires, causing over $1 million in damage.

I remember those riots. They put a friend of mine who ticks every SJ-interest box you can name in danger, because antifa do not actually care about the people they claim to care about.

I’m sure the Portland Police would like to do their jobs, but it’s not worth it–either they’ve been told not to by their superiors or they’re guaranteed to get sued if they do.

 

 

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Some Migration-Related Studies

I have too many tabs open on my computer, so here are some studies/writings which all touch on migration/population movements in some way:

Biographical Memoirs of Henry Harpending [pdf]:

The late Henry Harpending of West Hunter blog, along with Greg Cochran, wrote the 10,000 Year Explosion, did anthropological field work among the Ju/’hoansi, and pioneered population genetics. The biography has many interesting parts:

Henry’s early research on population genetics also helped establish the close relationship between genetics and geography. Genetic differences between groups tend to mirror the geographic distance between them, so that a map of genetic distances looks like a geographic map (Harpending and Jenkins, 1973). Henry developed methods for studying this relationship that are still in use. …

Meanwhile, Henry’s Kalahari field experience also motivated an interest in population ecology. Humans cope with variation in resource supply either by storage (averaging over time) or by mobility and sharing (averaging over space). These strategies are mutually exclusive. Those who store must defend their stored resources against others who would like to share them. Conversely, an ethic of sharing makes storage impossible. The contrast between the mobile and the sedentary Ju/’hoansi in Henry’s sample therefore represented a fundamental shift in strategy. …

Diseases need time to cause lesions on bone. If the infected individual dies quickly, no lesion will form, and the skeleton will look healthy. Lesions form only if the infected individual is healthy enough to survive for an extended period. Lesions on ancient bone may therefore imply that the population was healthy! …

In the 1970s, as Henry’s interest in genetic data waned, he began developing population genetic models of social evolution. He overturned 40 years of conventional wisdom by showing that group selection works best not when groups are isolated but when they are strongly connected by gene flow (1980, pp. 58-59; Harpending and Rogers, 1987). When gene flow is restricted, successful mutants cannot spread beyond the initial group, and group selection stalls.

Genetic Consequences of Social Stratification in Great Britain:

Human DNA varies across geographic regions, with most variation observed so far reflecting distant ancestry differences. Here, we investigate the geographic clustering of genetic variants that influence complex traits and disease risk in a sample of ~450,000 individuals from Great Britain. Out of 30 traits analyzed, 16 show significant geographic clustering at the genetic level after controlling for ancestry, likely reflecting recent migration driven by socio-economic status (SES). Alleles associated with educational attainment (EA) show most clustering, with EA-decreasing alleles clustering in lower SES areas such as coal mining areas. Individuals that leave coal mining areas carry more EA-increasing alleles on average than the rest of Great Britain. In addition, we leveraged the geographic clustering of complex trait variation to further disentangle regional differences in socio-economic and cultural outcomes through genome-wide association studies on publicly available regional measures, namely coal mining, religiousness, 1970/2015 general election outcomes, and Brexit referendum results.

Let’s hope no one reports on this as “They found the Brexit gene!”

Can you Move to Opportunity? Evidence from the Great Migration [PDF]:

The northern United States long served as a land of opportunity for black Americans, but today the region’s racial gap in intergenerational mobility rivals that of the South. I show that racial composition changes during the peak of the Great
Migration (1940-1970) reduced upward mobility in northern cities in the long run,
with the largest effects on black men. I identify urban black population increases
during the Migration at the commuting zone level using a shift-share instrument,
interacting pre-1940 black southern migrant location choices with predicted outmigration from southern counties. The Migration’s negative effects on children’s
adult outcomes appear driven by neighborhood factors, not changes in the characteristics of the average child. As early as the 1960s, the Migration led to greater white enrollment in private schools, increased spending on policing, and higher crime and incarceration rates. I estimate that the overall change in childhood environment induced by the Great Migration explains 43% of the upward mobility gap between black and white men in the region today.

43% is huge and, IMO, too big. However, the author may be on to something.

Lineage Specific Histories of Mycobacterium Tuberculosis Dispersal in Africa and Eurasia:

Mycobacterium tuberculosis (M.tb) is a globally distributed, obligate pathogen of humans that can be divided into seven clearly defined lineages. … We reconstructed M.tb migration in Africa and Eurasia, and investigated lineage specific patterns of spread. Applying evolutionary rates inferred with ancient M.tb genome calibration, we link M.tb dispersal to historical phenomena that altered patterns of connectivity throughout Africa and Eurasia: trans-Indian Ocean trade in spices and other goods, the Silk Road and its predecessors, the expansion of the Roman Empire and the European Age of Exploration. We find that Eastern Africa and Southeast Asia have been critical in the dispersal of M.tb.

I spend a surprising amount of time reading about mycobacteria.

Mysticism and Greater Male Variability

ctqda7fweae8tnbBuzzwords like “the male gaze” “objectification” “stereotype threat” “structural oppression” “white privilege” etc. are all really just re-hashings of the Evil Eye. We’ve shed the formal structure of religion but not the impulse for mystical thinking.

Today while debating with a friend about whether men or women have it better, it became plain that we were approaching the question from very different perspectives. He looked at men’s higher incomes and over-representation among CEOs and government officials and saw what I’ll call the mystical explanation: male oppression of women. I looked at the same data plus male over-representation among the homeless, mentally ill, suicides, and murder victims, and advocated the scientific explanation: greater male variability. 

What do I mean by mystical?

In primitive tribes, an accusation of witchcraft can quickly get you killed. What might inspire an accusation of witchcraft? A sick cow, a sudden death, a snake in a spot where it wasn’t yesterday, a drought, a flood, a twisted ankle–pretty much anything unexpected or unfortunate.

People understand cause and effect. Things happen because other things make them happen. But without a good scientific understanding of the world, the true causes of many events are unfindable, so people turn to mystical explanations. Why does it rain? Because a goddess is weeping. Why do droughts happen? Because someone forgot to make a sacrifice and angered the gods. Why do people get sick and die? Because other people cursed them.

If you’ve never encountered animist or mystical thought before, I recommend starting with some of my previous posts on the subject, which are thoroughly-researched and include lots of quotes from first-hand sources: Animism 1, 2, and 3; Aboriginal Witchcraft, more Australia 1, 2, and 3; mysticism and voodoo 1, 2, and 3. In this post I will be drawing on summaries of these and similar works.

A curse need not be deliberate. Simply being mad at someone or bearing them ill-will might be enough trigger the Evil Eye, curse them, and be forced by angry villagers to undo the curse–however the witchdoctor determines the curse must be undone. (This can be quite expensive.)

In animist thinking, things do not just happen. Things happen for reasons–usually malicious reasons.

In The Life and Adventure of William Buckley, 32 Years a Wanderer amongst the Aborigines, Buckley recounts: “They have an odd idea of death, for they do not suppose that any one dies from natural causes, but from human agencies: such as those to which I have alluded in previous pages of this narrative.”

The death of a companion via snakebite (probably a  common occurrence among people who walk barefoot in Australia) triggered a brutal “revenge” killing once it was determined who had cast the curse that motivated the snake:

“The cause of this sudden unprovoked cruelty was not, as usual, about the women, but because the man who had been killed by the bite of the snake belonged to the hostile tribe, and they believed my supposed brother-in-law carried about with him something that had occasioned his death. They have all sorts of fancies of this kind, and it is frequently the case, that they take a man’s kidneys out after death, tie them up in something, and carry them round the neck, as a sort of protection and valuable charm, for either good or evil.”

Buckley’s adoptive Aboriginal family, his sister and brother-in-law, who had been helping him since the tribe saved his life years ago, was killed in this incident.

“I should have been most brutally unfeeling, had I not suffered the deepest mental anguish from the loss of these poor people, who had all along been so kind and good to me. I am not ashamed to say, that for several hours my tears flowed in torrents, and, that for a long time I wept unceasingly. To them, as I have said before, I was as a living dead brother, whose presence and safety was their sole anxiety. Nothing could exceed the kindness these poor natives had shown me, and now they were dead, murdered by the band of savages I saw around me, apparently thirsting for more blood. Of all my sufferings in the wilderness, there was nothing equal to the agony I now endured.” …

“I returned to the scene of the brutal massacre; and finding the ashes and bones of my late friends, I scraped them up together, and covered them over with turf, burying them in the best manner I could, that being the only return I could make for their many kindnesses. I did so in great grief at the recollection of what they had done for me through so many years, and in all my dangers and troubles. ”

An account of Florence Young’s missionary work in the Solomon Islands (which are near Australia) recounts an identical justification for the cycle of violence on the Solomon Islands (which was quite threatening to Florence herself.) Every time someone died of any natural cause, their family went to the local witch doctor, who then used magic to determine who had used evil magic to kill the dead guy, and then the family would go and kill whomever the witch doctor indicated.

The advent of Christianity therefore caused a power struggle between the missionaries and the witch doctors, who were accustomed to being able to extort everyone and trick their followers into killing anyone who pissed them off. (See also Isaac Bacirongo’s account of the witch doctor who extorted his pre-pubescent sister as payment for a spell intended to kill Isaac’s wife–note: Isaac was not the one buying this spell; he likes his wife.)

So why do women make less money than men? Why are they underrepresented among CEOs and Governors and mathematicians? Something about the patriarchy and stereotype threat; something about men being evil.

Frankly, it sounds like men have the Evil Eye. A man thinks “Women are worse at math” and women suddenly become worse at math.

To be fair, my friend had only half the data, and when you have only half the data, the situation for men looks a lot better than the situation for women. But men aren’t only over-represented at the high ends of achievement–they’re also over-represented at the bottom. If patriarchy and stereotypes keep women from getting PhDs in math, why are little boys over-represented in special ed classes? Why are they more likely to be homeless, schizophrenic, commit suicide, or be murdered? Neither patriarchy nor male privilege can explain such phenomena.

Biology supplies us with a totally different explanation: greater male variability.

To review genetics, you have 23 pairs of chromosomes. Most of them are roughly X-shaped, except for the famous Y chromosome.

You have two chromosomes because you received one from each of your parents. Much of what the chromosomes do is redundant–for example, if you have blue eyes, then you received a gene for blue eyes from one parent and one from your other parent. One blue eye gene would be enough to give you blue eyes, but you have two.

Eye color isn’t terribly important, but things like how your immune system responds to threats or how your blood clots are. A rare mutation might make you significantly better or worse at these things, but the fact that you have two (or more) genes controlling each trait means that each very rare mutation tends to be paired with a more common version–lessening its effect.

There is, however, one big exception: the XY pair. Men don’t have a pair of Xs or a pair of Ys; they have one of each. If something is wrong on the X, the Y may have nothing to fix it, and vice versa.

The upshot is that if a man happens to get a gene that makes him extra tall, smart, conscientious, creative, charismatic, etc. somewhere on his X or Y chromosomes, he may not have a corresponding gene on the other chromosome to moderate its effects–and if he has a gene that makes him extra short, dumb, impulsive, dull, or anti-social, he is still unlikely to have a corresponding gene to dull the effect.

ci_generos
ASVAB scores: women in pink, men in blue.

Height is an uncontroversial example. Yes, the average man is taller than the average woman, but the spread of male heights is wider than the spread of female heights. More women are clustered around the average female height, while more men are both taller than the average man and shorter than the average man.

The graph to the right shows test scores from the Armed Services Vocational Aptitude Battery, but it shows the same basic idea: different means with women clustered more closely around average than men.

Whether the greater male variability hypothesis is true or not, it is an explanation that assumes no malice on anyone’s part. No one is maliciously forcing little boys into special ed, nor grown men into homelessness and suicide. The architecture of the XY and XX chromosome pairs is simply part of how humans are constructed.

But notice that you are much more likely to hear the theory that uses mysticism to blame people than the theory that doesn’t. One is tempted to think that some people are just inclined to assume that others are malicious–while ignoring other, more mundane explanations.

 

 

 

Best of EvX: How Turkic is Turkey?

 

dpfz16huuaatcs6
map of the spread of farming in Turkey/Anatolia/Europe

Hello my Turkish and Turkic readers! In honor of having written a lot on this blog, we’re taking a look back at our most popular posts, and today’s is on the genetic history of Turkey and the Turkic peoples.

Since my original post, I have learned many things about Turkey–mostly that Turks and other Turkic peoples love their culture and heritage. Note: I will probably use “Turkey” and “Anatolia”, interchangeably in this post. Turkey is the name for the modern state located in the region; Anatolia is a more generic name for the geography. I know that “Turkey” as a state or even a people didn’t exist 8,000 years ago.

Turkey has a long and fascinating history. It is possibly the cradle of civilization, as sites like Gobekli Tepe attest, and one of the birthplaces of agriculture.

1280px-j228y-dna29Early farmers spread out from Anatolia into Europe and Asia, contributing much of the modern European gene pool. There are many Y-DNA haplogroups in modern Turkey, which most likely means the Turkish male population hasn’t been completely replaced in recent invasions. (It’s not uncommon for an invasion to wipe out 80+% of the male population in an area.) About 24% of Turkish men carry haplogroup J2, which might not have originated in Turkey all of those centuries ago, but by 12,000 years ago it was common throughout Turkey (and today remains the most common haplogroup). This lineage spread with the Anatolian farmers into Europe around 8,000 years ago. and presumably Asia, as well.

TurkishDNA2fromHaak
From Haak et al

The second most common Y-haplogroup, at 16%, is good old R1b, which was carried into Turkey around 5-6,000 years ago by the Indo-European invaders. (The Indo-European invasion in Spain apparently wiped out all of the local men, but was not nearly so bad in Turkey.) These invaders spoke the Anatolian branch of the Indo-European tree, including Hittite and Luwian.

The Anatolian languages went extinct following Anatolia’s conquest by Alexander the Great in the 4th century BC (though it took several centuries for the languages to fall completely out of use.)

Haplogroup G–11%–is most common in the Caucasus, spread thinly over much of Anatolia and Iran, and even more thinly through Europe, North Africa, and central Asia. It’s probably a pretty old group–Otzi the Iceman was a member of the G clade.

Haplogroup E-M215 is found in about 10% of Turks and is most common in North Africa and the Horn of Africa, but is also quite common in Bedouin populations. It seems likely to be a very old haplogroup.

J1–9%–is common throughout the Middle East and amusingly reaches 46% among Jewish men named “Cohen.”

The rest of Turkish Y-chromosomes hail either from related haplogroups, like R1a, or represent smaller fractions of the population, like Q, 2%, commonly found in Siberia and Native Americans.

(Information on all Turkish Y-haplogroups.)

TurkmenSo how much Turkish DNA hails from Turkic peoples?

Modern Turks don’t speak Anatolian or Greek. They speak a Turkic language, which hails originally from an area near Mongolia. The Turkic-speaking peoples migrated into Anatolia around a thousand years ago, after a long migration/expansion through central Eurasia that culminated with the conquering of Constantinople. Today, the most notable Turkic-speaking groups are the Turks of Turkey,  AzerbaijanisUzbeksKazakhsTurkmen and Kyrgyz people.

The difficulty with tracing Turkic DNA is that, unlike the Mongols, Turkic DNA isn’t terribly homogeneous. The Mongols left a definite genetic signature wherever they went, but imparted less of their language–that is, they killed, raped, and taxed, but didn’t mix much with the locals. By contrast, the Turkic peoples seem to have mixed with their neighbors as they spread, imparting their language and probably not massacring too many people.

asia
Asian, Australian, and Melanesian ethic groups (including Indian, Middle Eastern, and Chinese) from Haak et al’s dataset

According to Wikipedia:

The largest autosomal study on Turkish genetics (on 16 individuals) concluded the weight of East Asian (presumably Central Asian) migration legacy of the Turkish people is estimated at 21.7%.[1]

Note that Turkey shares haplogroup J2 with its Turkic neighbors. This raises an interesting possibility: early Anatolian farmers spread into central Eurasia, mixed with local nomadic Turkic speakers, and then migrated back into Turkey. But 16 people isn’t much of a study.

“South Asian contribution to Turkey’s population was significantly higher than East/Central Asian contributions, suggesting that the genetic variation of medieval Central Asian populations may be more closely related to South Asian populations, or that there was continued low level migration from South Asia into Anatolia.”

“South Asian” here I assume means that Turkey looks more like Iran than Uzbekistan, which is true. The Turkic wanderers likely passed through Iran on their way to Turkey, picking up Iranian culture (such as Islam) and DNA–plus the pre-existing Anatolian population was probably closer to Iran than Uzbekistan anyway.

… the exact kinship between current East Asians and the medieval Oghuz Turks is uncertain. For instance, genetic pools of Central Asian Turkic peoples is particularly diverse and modern Oghuz Turkmens living in Central Asia are with higher West Eurasian genetic component than East Eurasian.[2][3][4]

I think “West Eurasian” is a euphemism for “Caucasian.” East Eurasian (aka Asian) DNA, you can see in the map above, tends to be red+yellow, tending toward all red in Siberia and all yellow in Taiwan. Indo-European groups, including Iranians, tend to have a teal/blue/orange pattern. Turkmen, Uzbeks, and Uygurs, as you can see in the graph, have a combination of both sets of DNA. The Turks also have a small amount of east Asian DNA–but much less–while their neighbors in Iran and central Eurasia share a little Indian DNA.

Several studies have concluded that the genetic haplogroups indigenous to Western Asia have the largest share in the gene pool of the present-day Turkish population.[5][6][7][8][5][9][10][11] An admixture analysis determined that the Anatolian Turks share most of their genetic ancestry with non-Turkic populations in the region and the 12th century is set as an admixture date.[12]

Western Asia=Middle East.

So Turkish DNA is about 22% Turkic, from nomads who entered the country via Iran, and about 78% ancient Anatolian, from the people who had already lived there on the Anatolian plateau for centuries.

But as the Turkic peoples (and many of the comments on my original post) show, culture doesn’t have to be genetic, and many Turkic people feel a strong cultural connection to each other. (And many people report that various Turkic languages are pretty easy to understand if you speak one Turkic language–EG:

hello everyone I’m an Uzbek,

… tatars played a great role in Genghis’s empire and they had an empire after dividing the empire called Golden Horde, it was mongol state but after it became to turki with a time. and their sons are kazakh and kirgiz. Thats why we uzbeks can understand turkish easly more than our neighboors kazakhs. and we uzbeks are not mongoloid like kazakhs.because uzbek language has oghuz and karluk dialect. uzbek-uygur are like turkish-azerbaijani or turkish-crimean tatar. thats why uzbek dialect is most understandable language for every turkic people. but we can understand %95 uygur, %85 turkish-turkmen, %70 azerbaijani %50 kazakh.

Our Uzbeki friend’s full comment is very interesting, and I recommend you read the whole thing.

For that matter, many thanks to everyone who has left interesting comments sharing your family’s histories or personal perspectives on Turkish/Turkic culture and history over the years–I hope you have enjoyed this update.

Greatest Hits: Native Americans and Neanderthal DNA.

Native-American-populations
Source: Ancient Beringians: A Discovery Changing Early Native American History

Over the years, a few of my posts have been surprisingly popular–Turkey: Not very Turkic, Why do Native Americans Have so much Neanderthal DNA?, Do Black Babies have Blue Eyes? and Can Ice packs help stop a seizure (in humans)?

It’s been a while since these posts aired, so I thought it was time to revisit the material and see if anything new has turned up.

Today, lets revisit Native Americans and Neanderthal DNA:

I’m sorry, but I no longer think Native Americans (aka American Indians) have higher than usual levels of Neanderthal DNA. Sorry. Their Neanderthal DNA levels are similar to (but slightly lower than) those of other members of the Greater Asian Clade. They also have a small amount of Denisovan DNA–at least some of them.

Why the confusion? Some Neanderthal-derived alleles are indeed more common in Native Americans than in other peoples. For example, the Neanderthal derived allele SLC16A11 occurs in 10% of sampled Chinese, 0% of Europeans, and 50% of sampled Native Americans. (Today, this gene makes people susceptible to Type 2 diabetes, but it must have been very useful to past people to be found in such a large percent of the population.)

neanderthalmap

And there was one anomalously high Neanderthal DNA measure in Natives living near the Great Slave Lake, Canada. (Look, I didn’t name the lake.)

But this doesn’t mean all Native Americans possess all Neanderthal alleles in greater quantities.

So how much Neanderthal do Native Americans have? Of course, we can’t quite be sure, especially since only a few Neanderthals have even had their DNA analyzed, and with each new Neanderthal sequenced, we have more DNA available to compare against human genomes. But here are some estimates:

beautifulneanderthalDenisovan
Neanderthal and Denisovan contributions to different populations by chromosome (source)

 et al, in The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans, report:

Native Americans: 1.37%
Central Asia: 1.4%
East Asia: 1.39%
Oceana (Melanesians): 1.54%
South Asia: 1.19%
Europeans: 1.06%

I have seen it claimed that the high Neanderthal percents for Oceanan populations (that is, Melanesians and their relatives,) could be a result of Denisovan DNA being incompletely distinguished from Neanderthal.

Prufer et al, [pdf] 2017, report somewhat higher values:

East Asians: 2.3–2.6%
Europeans: 1.8–2.4%

While Lohse and Frantz estimate an even higher rate of between 3.4–7.3% for Europeans and East Asians. (They found 5.9% in their Chinese sample and 5.3% in their European.)

The Mixe and Karitiana people of Brazil have 0.2% Denisovan (source); other estimates for the amount of Denisovan DNA in Native populations are much lower–ie, 0.05%.

I found an older paper by Prufer et al with estimates for three Hispanic populations, but doesn’t clarify if they have Native American ancestry:

CLM–Colombians from Medellin: 1.14%
MXL–Mexicans in LA: 1.22%
PUR–Puerto Rico: 1.05%

Since this is an older paper, all of its estimates may be on the low side.

The absolute values of these numbers is probably less important than the overall ratios, since the numbers themselves are still changing as more Neanderthal DNA is uncovered. The ratios in different papers point to Native Americans having, overall, about the same amount of Neanderthal DNA as their relatives in East Asia.

Melanesians, though. There’s an interesting story lying in their DNA.

Book Club: The Code Economy: The DNA of Business

“DNA builds products with a purpose. So do people.” –Auerswald, The Code Economy

McDonald’s is the world’s largest restaurant chain by revenue[7], serving over 69 million customers daily in over 100 countries[8] across approximately 36,900 outlets as of 2016.[9] … According to a BBC report published in 2012, McDonald’s is the world’s second-largest private employer (behind Walmart with 1.9 million employees), 1.5 million of whom work for franchises. …

There are currently a total of 5,669 company-owned locations and 31,230 franchised locations… Notably, McDonald’s has increased shareholder dividends for 25 consecutive years,[18] making it one of the S&P 500 Dividend Aristocrats.[19][20]

According to Fast Food Nation by Eric Schlosser (2001), nearly one in eight workers in the U.S. have at some time been employed by McDonald’s. … Fast Food Nation also states that McDonald’s is the largest private operator of playgrounds in the U.S., as well as the single largest purchaser of beef, pork, potatoes, and apples.  (Wikipedia)

How did a restaurant whose only decent products are french fries and milkshakes come to dominate the global corporate landscape?

IKEA is not only the world’s largest furniture store, but also among the globe’s top 10 retailers of anything and the 25th most beloved corporation. (Disney ranks number one.) Even I feel a strange, heartwarming emotion at the thought of IKEA, which somehow comes across as a sweet and kind multi-national behemoth.

In The Code Economy, Auerswald suggests that the secret to McDonald’s success isn’t (just) the french fries and milkshake machines:

Kroc opened his first McDonald’s restaurant in 1955 in Des Plaines, California. Within five years he had opened two hundred new franchises across the country. [!!!] He pushed his operators obsessively to adhere to a system that reinforced the company motto: “Quality, service, cleanliness, and value.”

h/t @simongerman600

Quoting Kroc’s1987 autobiography,

“It’s all interrelated–our development of the restaurant, the training, the marketing advice, the product development, the research that has gone into each element of the equipment package. Together with our national advertising and continuing supervisory assistance, it forms an invaluable support system. Individual operators pay 11.5 percent of their gross to the corporation for all of this…”

The process of operating a McDonald’s franchise was engineered to be as cognitively undemanding as possible. …

Kroc created a program that could be broken into subroutines…. Acting like the DNA of the organization, the manual allowed the Speedee Service System to function in a variety of environments without losing essential structure or function.

McDonald’s is big because it figured out how to reproduce.

source: Statista

I’m not sure why IKEA is so big (I don’t think it’s a franchise like McDonald’s,) but based on the information posted on their walls, it’s because of their approach to furniture design. First, think of a problem, eg, People Need Tables. Second, determine a price–IKEA makes some very cheap items and some pricier items, to suit different customers’ needs. Third, use Standard IKEA Wooden Pieces to design a nice-looking table. Fourth, draw the assembly instructions, so that anyone, anywhere, can assemble the furniture themselves–no translation needed.

IKEA furniture is kind of like Legos, in that much of it is made of very similar pieces of wood assembled in different ways. The wooden boards in my table aren’t that different in size and shape from the ones in my dresser nor the ones in my bookshelf, though the items themselves have pretty different dimensions. So on the production side, IKEA lowers costs by producing not actual furniture, but collections of boards. Boards are easy to make–sawmills produce tons of them.

Furniture is heavy, but mostly empty space. By contrast, piles of boards stack very neatly and compactly, saving space both in shipping and when buyers are loading the boxes into their cars. (I am certain that IKEA accounts for common car dimensions in designing and packing their furniture.)

And the assembly instruction allow the buyer to ultimately construct the furniture.

In other words, IKEA has hit upon a successful code that allows them to produce many different designs from a few basic boards and ship them efficiently–keeping costs low and allowing them to thrive.

From Anatomy of an IKEA product:

The company is also looking for ways to maximize warehouse efficiency.

“We have (only) two pallet sizes,” Marston said, referring to the wooden platforms on which goods are placed. “Our warehouses are dimensioned and designed to hold these two pallet sizes. It’s all about efficiencies because that helps keep the price of innovation down.”

In Europe, some IKEA warehouses utilize robots to “pick the goods,” a term of art for grabbing products off very high shelves.

These factories, Marston said, are dark, since no lighting is needed for the robots, and run 24 hours a day, picking and moving goods around.

“You (can) stand on a catwalk,” she said, “and you look out at this huge warehouse with 12 pallets (stacked on top of each other) and this robot’s running back and forth running on electronic eyebeams.”

IKEA’s code and McDonald’s code are very different, but both let the companies produce the core items they sell quickly, cheaply, and efficiently.

In The Code Economy, Chapter 8: Evolution, discusses the rise of Tollhouse Cookies, McDonald’s, the difference between natural and artificial objects, and the development of evolutionary theory from Darwin through Watson and Crick and through to Kauffman and Levine’s 1987 paper, “Toward a General Theory of Adaptive Walks on Rugged Landscapes.” (With a brief stop at Erwin Shrodinger along the way.)

The difficulty with evolution is that systems are complicated; successful mutations or even just combinations of existing genes must work synergistically with all of the other genes and systems already operating in the body. A mutation that increases IQ by tweaking neurons in a particular way might have the side effect of causing neurons outside the brain to malfunction horribly; a mutation that protects against sickle-cell anemia when you have one copy of it might just kill you itself if you have two copies.

Auerswald quotes Kauffman and Levin:

“Natural selection does not work as an engineer works… It works like a tinkereer–a tinkerer who does not know exactly what he is going to produce but uses… everything at his disposal to produce some kind of workable object.” This process is progressive, moving form simpler to more complex forms: “Evolution doe not produce novelties from scratch. It works on what already exists, either transforming a system to give it new functions or combining several systems to produce a more elaborate one [as] during the passage from unicellular to multicellular forms.”

Further:

The Kauffman and Levin model was as simple as it was powerful. Imagine a genetic code of length N, where each gene might occupy one of two possible “states”–for example, “o” and “i” in a binary computer. The difficulty of the evolutionary problem was tunable with the parameter K, which represented the average number of interactions among genes. The NK model, as it came to be called, was able to reproduce a number of measurable features of evolution in biological systems. Evolution could be represented as a genetic walk on a fitness landscape, in which increasing complexity was now a central parameter.

You may remember my previous post on Local Optima, Diversity, and Patchwork:

Local optima–or optimums, if you prefer–are an illusion created by distance. A man standing on the hilltop at (approximately) X=2 may see land sloping downward all around himself and think that he is at the highest point on the graph. But hand him a telescope, and he discovers that the fellow standing on the hilltop at X=4 is even higher than he is. And hand the fellow at X=4 a telescope, and he’ll discover that X=6 is even higher.

A global optimum is the best possible way of doing something; a local optimum can look like a global optimum because all of the other, similar ways of doing the same thing are worse.

Some notable examples of cultures that were stuck at local optima but were able, with exposure, to jump suddenly to a higher optima: The “opening of Japan” in the late 1800s resulted in breakneck industrialization and rising standards of living; the Cherokee invented their own alphabet (technically a syllabary) after glimpsing the Roman one, and achieved mass literacy within decades; European mathematics and engineering really took off after the introduction of Hindu-Arabic numerals and the base-ten system.

If we consider each culture its own “landscape” in which people (and corporations) are finding locally optimal solutions to problems, then it becomes immediately obvious that we need both a large number of distinct cultures working out their own solutions to problems and occasional communication and feedback between those cultures so results can transfer. If there is only one, global, culture, then we only get one set of solutions–and they will probably be sub-optimal. If we have many cultures but they don’t interact, we’ll get tons of solutions, and many of them will be sub-optimal. But many cultures developing their own solutions and periodically interacting can develop many solutions and discard sub-optimal ones for better ones.

On a related note, Gore Burnelli writes: How Nassim Taleb changed my mind about religion:

Life constantly makes us take decisions under conditions of uncertainty. We can’t simply compute every possible outcome, and decide with perfect accuracy what the path forward is. We have to use heuristics. Religion is seen as a record of heuristics that have worked in the past. …

But while every generation faces new circumstances, there are also some common problems that every living being is faced with: survival and reproduction, and these are the most important problems because everything else depends on them. Mess with these, and everything else becomes irrelevant.

This makes religion an evolutionary record of solutions which persisted long enough, by helping those who held them to persist.

This is not saying “All religions are perfect and good and we should follow them,” but it is suggesting, “Traditional religions (and cultures) have figured out ways to solve common problems and we should listen to their ideas.”

From Ray Kurzweil

Back in The Code Economy, Auerswald asks:

Might the same model, derived from evolutionary biology, explain the evolution of technology?

… technology may also be nothing else but the capacity for invariant reproduction. However, in order for more complex forms of technology to be viable over time, technology also must possess a capacity for learning and adaptation.

Evolutionary theory as applied to the advance of code is the focus of the next chapter. Kauffman and Levin’s NK model ends up providing a framework for studying the creation and evolution of code. Learning curves act as the link between biology and economics.

Will the machines become sentient? Or McDonald’s? And which should we worry about?

A Response to Epigenetics and Ethics: Rights and Consequences

Dr. Robison–author of Epigenetics and Public Policy–asks and essential question: Where does the right to swing one’s epigenome end? Or as he puts it:

If epigenetics does introduce scientific novelties to the conventional understanding of biology, then according to the model it also has equally significant ethical and political implications.

What responsibility do I–as an egg-bearing person–have to ensure the health of my children and grandchildren’s epigenenomes? Society affirms my right to smoke cigarettes, even though they may give me cancer down the road–it’s my body and I am allowed to do what I wish with it. But what if my smoking cigarettes today causes cancer in a future, as yet unborn grandchild whom I never meet? What about her right to chose not to be exposed to carcinogens? Who am I to take that from her–and what right has society, the government, or anyone else to tell me what I may or may not do with my own body in the interests of some future people who may never come into existence?

I am summarizing, perhaps badly; you may read the whole post over on Dr. Robison’s blog. (Of course Robison is himself trying to summarize an argument I am sure he lays out in much more detail in his book.)

Here is my hastily written response, in the interest of clear conversational threading:

I’m not sure epigenetics constitutes such a fundamental shift in our understandings of genetics and inheritance as to actually warrant much change in our present policies. For example, you question whether policies should be enacted to restrict a 12 yr old girl’s right to eat what she wishes in defense of her unborn grandchild’s epigenome, but we today don’t even restrict a pregnant woman’s right to drink or smoke. Cocaine is illegal, but last time I checked, women didn’t go to prison for giving birth to crack babies. For that matter, women are allowed to kill unborn babies. I’m not commenting pro or against abortion, just noting that it is legal and most people consider death kind of a big deal. So I don’t think society is about to start outlawing stuff because of its negative effects two generations down the road.

On the other hand, if you look at the data on smoking, rates have definitely been falling ever since the tobacco-cancer link became news. The gov’t didn’t have to outlaw smoking for a lot of women to stop smoking for their children’s health.

But let’s return to the philosophical argument. All men are created equal… or are they? I do not think the Founding Fathers ever meant equality in a genetic sense. They could see with their own eyes that some men were tall and others short, some wise and others foolish, some virtuous and others criminal. They could see see that sons and daughters took after their parents and that a great many people started life in horribly unfair circumstances while others lived in luxury. They could see the cruel unfairness of disease, disability, and early death. Their rejection was not of biological or factual inequalities but of spiritual inequality. They rejected the notion that some men are created special by God to rule over others, and some men are created inferior by God, to be ruled over.

You state, “However, the evidence emerging from epigenetics suggests this is not the case. Instead of individuals of each generation being born with a pristine copy of their biological essence, they are inheriting a genetic endowment riddled with markers of the experiences of their parents and grandparents and great-grandparents, and so on. And these inherited epigenetic markers, as more and more research is showing, are having direct effects on the physical and mental health of individuals from causes not actually experienced by these individuals.”

I think there is a mistake here in regarding genetics as “pristine” in some form. What if my mother is an anxious person, and I, through environmental exposure, grow into a similarly anxious person? What if my mother has a gene for anxiety, and I inherit it? What if I possess a de novo genetic mutation that causes me to be anxious? And what if I suffer a genetic deletion in one of my chromosomes that causes anxiety? How is any of this different, functionally, from some trauma my mother suffered (say, a car accident) causing epigenetic changes that are subsequently passed on to me?

What is pristine about Down’s Syndrome, Williams’, or Klinefelter’s? Or just having the random bad luck to get genes for short, dumb, and ugly?

“For example, research in epigenetics shows that the choices and experiences of individuals in one generation are conditioning the basic nature of individuals of subsequent generations, which indelibly affects how those new individuals will exercise their own rights. ”

It can’t be indelible. For starters, you only inherit half of each parent’s genome–thus half their epigenome. So right there’s a 50% chance you won’t inherit any particular epigenetic marker. By gen two we’re talking 25% chance, and that’s not counting the constant re-writing of our epigenomes. However, I don’t think the policy implications for countries are all that different from our current thinking. We can say, for example, “If we have X level of pollution in the water, then Y number of people will get cancer,” and it’s a public health problem even if we don’t know “they’ll get cancer because of epigenetics.”

So let’s broaden the inquiry a bit. Not how does epigenetics impact classical liberalism (which is behind us, anyway,) but how do genetics, epigenetics, heritability, et at all influence our modern sensibilities? Modern liberalism is built almost as a reaction against former racialist notions of “blood”, with a consequent belief that people are, on average, about genetically equal. This butts up against the realization that some people are gifted and talented from birth, which many people quietly rationalize away while knowing they are being a bit dishonest, perhaps on the grounds that this is tantamount to statistical noise.

But the whole notion of “meritocracy” becomes more problematic if we admit that there’s a large genetic (or accidental, or environmental, or anything outside of free will,) contribution to IQ, educational attainment, mental illness, your chances of getting a good job, how other people treat you (because of attractiveness,) etc. Should a person who is dumb through no fault of their own suffer poverty? Should an ugly person be denied a job or a date? There’s an essential unfairness to it, after all.

But by the same token, what are you going to do about it? Declare that everyone under a certain IQ gets free money? What sort of incentives does that set up for society? And what does it do to someone’s self-image if they are Officially Delcared Stupid?

But this is all focused on the negative. What if we find ways to make people smarter, healthier, stronger? I think we’d take them. Sure, we’d have a few hold-outs who worry about “playing god,” (much as today we have people who worry about vaccines despite the massive health improvements public vaccination campaigns have cause.) But in the end we’d take them. Similarly, in the end, I think most people would try to avoid damaging their descendants’ epigenomes–even if not through direct public policy.

 

Addendum: while I am skeptical of most claims about epigenetics, eg, people claiming that epigenetic trauma can be transmitted for over a century, there do seem to be some things that cause what we can here characterize as multi-generational epigenetic effects. For example, the drug diethylstilbestrol (DES), given to pregnant women to prevent miscarriages back in the 70s, not only causes cancer in the women it was given to, but also in their daughters. (It also results in intersex disorders in male fetuses.) In the third generation (that is, the sons daughters of the fetuses that were exposed to DES their mothers took during pregnancy,) there are still effects, like an increased risk of irregular periods. This is not necessarily “epigenetic” but similar enough to include in the conversation.

When did language evolve?

The smartest non-human primates, like Kanzi the bonobo and Koko the gorilla, understand about 2,000 to 4,000 words. Koko can make about 1,000 signs in sign language and Kanzi can use about 450 lexigrams (pictures that stand for words.) Koko can also make some onomatopoetic words–that is, she can make and use imitative sounds in conversation.

A four year human knows about 4,000 words, similar to an exceptional gorilla. An adult knows about 20,000-35,000 words. (Another study puts the upper bound at 42,000.)

Somewhere along our journey from ape-like hominins to homo sapiens sapiens, our ancestors began talking, but exactly when remains a mystery. The origins of writing have been amusingly easy to discover, because early writers were fond of very durable surfaces, like clay, stone, and bone. Speech, by contrast, evaporates as soon as it is heard–leaving no trace for archaeologists to uncover.

But we can find the things necessary for speech and the things for which speech, in turn, is necessary.

The main reason why chimps and gorillas, even those taught human language, must rely on lexigrams or gestures to communicate is that their voiceboxes, lungs, and throats work differently than ours. Their semi-arborial lifestyle requires using the ribs as a rigid base for the arm and shoulder muscles while climbing, which in turn requires closing the lungs while climbing to provide support for the ribs.

Full bipedalism released our early ancestors from the constraints on airway design imposed by climbing, freeing us to make a wider variety of vocalizations.

Now is the perfect time to break out my file of relevant human evolution illustrations:

Source: Scientific American What Makes Humans Special

We humans split from our nearest living ape relatives about 7-8 million years ago, but true bipedalism may not have evolved for a few more million years. Since there are many different named hominins, here is a quick guide:

Source: Macroevolution in and Around the Hominin Clade

Australopithecines (light blue in the graph,) such as the famous Lucy, are believed to have been the first fully bipedal hominins, although, based on the shape of their toes, they may have still occasionally retreated into the trees. They lived between 4 and 2 million years ago.

Without delving into the myriad classification debates along the lines of “should we count this set of skulls as a separate species or are they all part of the natural variation within one species,” by the time the homo genus arises with H Habilis or H. Rudolfensis around 2.8 million years ag, humans were much worse at climbing trees.

Interestingly, one direction humans have continued evolving in is up.

Oldowan tool

The reliable production of stone tools represents an enormous leap forward in human cognition. The first known stone tools–Oldowan–are about 2.5-2.6 million years old and were probably made by homo Habilis. These simple tools are typically shaped only one one side.

By the Acheulean–1.75 million-100,000 years ago–tool making had become much more sophisticated. Not only did knappers shape both sides of both the tops and bottoms of stones, but they also made tools by first shaping a core stone and then flaking derivative pieces from it.

The first Acheulean tools were fashioned by h Erectus; by 100,000 years ago, h Sapiens had presumably taken over the technology.

Flint knapping is surprisingly difficult, as many an archaeology student has discovered.

These technological advances were accompanied by steadily increasing brain sizes.

I propose that the complexities of the Acheulean tool complex required some form of language to facilitate learning and teaching; this gives us a potential lower bound on language around 1.75 million years ago. Bipedalism gives us an upper bound around 4 million years ago, before which our voice boxes were likely more restricted in the sounds they could make.

A Different View

Even though “homo Sapiens” has been around for about 300,000 years (or so we have defined the point where we chose to differentiate between our species and the previous one,) “behavioral modernity” only emerged around 50,000 years ago (very awkward timing if you know anything about human dispersal.)

Everything about behavioral modernity is heavily contested (including when it began,) but no matter how and when you date it, compared to the million years or so it took humans to figure out how to knap the back side of a rock, human technologic advance has accelerated significantly over the past 100,000 and even moreso over the past 50,000 and even 10,000.

Fire was another of humanity’s early technologies:

Claims for the earliest definitive evidence of control of fire by a member of Homo range from 1.7 to 0.2 million years ago (Mya).[1] Evidence for the controlled use of fire by Homo erectus, beginning some 600,000 years ago, has wide scholarly support.[2][3] Flint blades burned in fires roughly 300,000 years ago were found near fossils of early but not entirely modern Homo sapiens in Morocco.[4] Evidence of widespread control of fire by anatomically modern humans dates to approximately 125,000 years ago.[5]

What prompted this sudden acceleration? Noam Chomsky suggests that it was triggered by the evolution of our ability to use and understand language:

Noam Chomsky, a prominent proponent of discontinuity theory, argues that a single chance mutation occurred in one individual in the order of 100,000 years ago, installing the language faculty (a component of the mind–brain) in “perfect” or “near-perfect” form.[6]

(Pumpkin Person has more on Chomsky.)

More specifically, we might say that this single chance mutation created the capacity for figurative or symbolic language, as clearly apes already have the capacity for very simple language. It was this ability to convey abstract ideas, then, that allowed humans to begin expressing themselves in other abstract ways, like cave painting.

I disagree with this view on the grounds that human groups were already pretty widely dispersed by 100,000 years ago. For example, Pygmies and Bushmen are descended from groups of humans who had already split off from the rest of us by then, but they still have symbolic language, art, and everything else contained in the behavioral modernity toolkit. Of course, if a trait is particularly useful or otherwise successful, it can spread extremely quickly (think lactose tolerance,) and neither Bushmen nor Pygmies were 100% genetically isolated for the past 250,000 years, but I simply think the math here doesn’t work out.

However, that doesn’t mean Chomsky isn’t on to something. For example, Johanna Nichols (another linguist,) used statistical models of language differentiation to argue that modern languages split around 100,000 years ago.[31] This coincides neatly with the upper bound on the Out of Africa theory, suggesting that Nichols may actually have found the point when language began differentiating because humans left Africa, or perhaps she found the origin of the linguistic skills necessary to accomplish humanity’s cross-continental trek.

Philip Lieberman and Robert McCarthy looked at the shape of Neanderthal, homo Erectus, early h Sapiens and modern h Sapiens’ vocal tracts:

In normal adults these two portions of the SVT form a right angle to one another and are approximately equal in length—in a 1:1 proportion. Movements of the tongue within this space, at its midpoint, are capable of producing tenfold changes in the diameter of the SVT. These tongue maneuvers produce the abrupt diameter changes needed to produce the formant frequencies of the vowels found most frequently among the world’s languages—the “quantal” vowels [i], [u], and [a] of the words “see,” “do,” and “ma.” In contrast, the vocal tracts of other living primates are physiologically incapable of producing such vowels.

(Since juvenile humans are shaped differently than adults, they pronounce sounds slightly differently until their voiceboxes fully develop.)

Their results:

…Neanderthal necks were too short and their faces too long to have accommodated equally proportioned SVTs. Although we could not reconstruct the shape of the SVT in the Homo erectus fossil because it does not preserve any cervical vertebrae, it is clear that its face (and underlying horizontal SVT) would have been too long for a 1:1 SVT to fit into its head and neck. Likewise, in order to fit a 1:1 SVT into the reconstructed Neanderthal anatomy, the larynx would have had to be positioned in the Neanderthal’s thorax, behind the sternum and clavicles, much too low for effective swallowing. …

Surprisingly, our reconstruction of the 100,000-year-old specimen from Israel, which is anatomically modern in most respects, also would not have been able to accommodate a SVT with a 1:1 ratio, albeit for a different reason. … Again, like its Neanderthal relatives, this early modern human probably had an SVT with a horizontal dimension longer than its vertical one, translating into an inability to reproduce the full range of today’s human speech.

It was only in our reconstruction of the most recent fossil specimens—the modern humans postdating 50,000 years— that we identified an anatomy that could have accommodated a fully modern, equally proportioned vocal tract.

Just as small children who can’t yet pronounce the letter “r” can nevertheless make and understand language, I don’t think early humans needed to have all of the same sounds as we have in order to communicate with each other. They would have just used fewer sounds.

The change in our voiceboxes may not have triggered the evolution of language, but been triggered by language itself. As humans began transmitting more knowledge via language, humans who could make more sounds could utter a greater range of words perhaps had an edge over their peers–maybe they were seen as particularly clever, or perhaps they had an easier time organizing bands of hunters and warriors.

One of the interesting things about human language is that it is clearly simultaneously cultural–which language you speak is entirely determined by culture–and genetic–only humans can produce language in the way we do. Even the smartest chimps and dolphins cannot match our vocabularies, nor imitate our sounds. Human infants–unless they have some form of brain damage–learn language instinctually, without conscious teaching. (Insert reference to Steven Pinker.)

Some kind of genetic changes were obviously necessary to get from apes to human language use, but exactly what remains unclear.

A variety of genes are associated with language use, eg FOXP2. H Sapiens and chimps have different versions of the FOXP2 gene, (and Neanderthals have a third, but more similar to the H Sapiens version than the chimp,) but to my knowledge we have yet to discover exactly when the necessary mutations arose.

Despite their impressive skulls and survival in a harsh, novel climate, Neanderthals seem not to have engaged in much symbolic activity, (though to be fair, they were wiped out right about the time Sapiens really got going with its symbolic activity.) Homo Sapiens and Homo Nanderthalis split around 800-400,000 years ago–perhaps the difference in our language genes ultimately gave Sapiens the upper hand.

Just as farming appears to have emerged relatively independently in several different locations around the world at about the same time, so behavioral modernity seems to have taken off in several different groups around the same time. Of course we can’t rule out the possibility that these groups had some form of contact with each other–peaceful or otherwise–but it seems more likely to me that similar behaviors emerged in disparate groups around the same time because the cognitive precursors necessary for those behaviors had already begun before they split.

Based on genetics, the shape of their larynges, and their cultural toolkits, Neanderthals probably did not have modern speech, but they may have had something similar to it. This suggests that at the time of the Sapiens-Neanderthal split, our common ancestor possessed some primitive speech capacity.

By the time Sapiens and Neanderthals encountered each other again, nearly half a million years later, Sapiens’ language ability had advanced, possibly due to further modification of FOXP2 and other genes like it, plus our newly modified voiceboxes, while Neanderthals’ had lagged. Sapiens achieved behavioral modernity and took over the planet, while Neanderthals disappeared.

 

Trying to be Smart: on bringing up extremely rare exceptions to prove forests don’t exist, only trees

When my kids don’t want to do their work (typically word problems in math,) they start coming up with all kinds of crazy scenarios to try to evade the question. “What if Susan cloned herself?” “What if Joe is actually the one driving the car, and he only saw the car pass by because he was looking at himself in a mirror?” “What if John used a wormhole to travel backwards in time and so all of the people at the table were actually Joe and so I only need to divide by one?” “What if Susan is actually a boy but her parents accidentally gave him the wrong name?” “What if ALIENS?”

After banging my head on the wall, I started asking, “Which is more likely: Sally and Susan are two different people, or Sally cloned herself, something no human has ever done before in the 300,000 years of homo Sapiens’ existence?” And sometimes they will, grudgingly, admit that their scenarios are slightly less likely than the assumptions the book is making.*

I forgive my kids, because they’re children. When adults do the same thing, I am much less sympathetic.

Folks on all sides of the political spectrum are probably guilty of this, but my inclinations/bubble lead me to encounter certain ones more often. Sex/gender is a huge one (even I have been led astray by sophistry on this subject, for which I apologize.)

Over in biology, sex is simply defined: Females produce large gametes. Males produce small gametes. It doesn’t matter how gametes are produced. It doesn’t matter what determines male or femaleness. All that matters is gamete size. There is no such thing (at least in humans) as a sex “spectrum”: reproduction requires one small gamete and one large gamete. Medium-sized gametes are not part of the process.

About 99.9% of people fit into the biological categories of “male” and “female.” An extremely small minority (<1%) have rare biological issues that interfere with gamete formation–people with Klinefelter’s, for example, are genetically XXY instead of XX or XY. People with Klinefelter’s are also infertile–unlike large gametes and small gametes, XXY isn’t part of a biological reproduction strategy. Like trisomy 21, it’s just an unfortunate accident in cell division.

In a mysterious twist, the vast majority of people have a “gender” identity that matches their biological sex. Even female athletes–women who excel at a stereotypically and highly masculine field–tend to identify as “women,” not men. Even male fashion designers tend to self-identify as men. There are a few people who identify as transgender, but in my personal experience, most of them are actually intersex in some way (eg, a woman who has autism, a condition characterized as “extreme male brain,” may legitimately feel like she thinks more like a guy than a girl.) Again, this is an extremely small percent of the population. For 99% of people you meet, normal gender assumptions apply.

So jumping into a conversation about “men” and “women” with “Well actually, ‘men’ and ‘women’ are just social constructs and gender is actually a spectrum and there are many different valid gender expressions–” is a great big NO.

Jumping into a discussion of women’s issues (like childbirth) with “Actually, men can give birth, too,” or the Women’s March with “Pussyhats are transphobic because some women have penises; vaginas don’t define what it means to be female,” is an even bigger NO, and I’m not even a fan of pussyhats.

Only biological females can give birth. That’s how the species works. When it comes to biology, leave things that you admit aren’t biology at the door. If a transgender man with a uterus gives birth to a child, he is still a biological female and we don’t need to confuse things by implying that someone gestated a fetus in his testicles. Over the millennia that humans have existed, a handful of people with some form of biological chimerism (basically, an internalized conjoined twin who never fully developed but ended up contributing an organ or two) who thought of themselves as male may have nonetheless given birth. These cases are so rare that you will probably never meet someone with them in your entire life.

Having lost a leg due to an accident (or 4 legs, due to being a pair of conjoined twins,) does not make “number of legs in humans” a spectrum ranging from 0-4. Humans have 2 legs; a few people have unfortunate accidents. Saying so doesn’t imply that people with 0 legs are somehow less human. They just had an accident.

In a conversation I read recently, Person A asserted that if two blue-eyed parents had a brown-eyed baby, the mother would be suspected of infidelity. A whole bunch of people immediately jumped on Person A, claiming he was scientifically ignorant and hadn’t paid attention in school–sadly, these overconfident people are actually the ones who don’t understand genetics, because blue eyes are recessive and thus two blue eyed people can’t make a brown-eyed biological child.  A few people, however, asserted that Person A was scientifically illiterate because there is an extremely rare brown-eyed gene that two blue-eyed people can carry, resulting in a brown-eyed child.

But this is not scientific illiteracy. The recessive brown-eyed gene is extremely rare, and both parents would have to have it. Infidelity, by contrast, is much more common. It’s not that common, but it’s more common than two parent both having recessive brown-eyed genes. Insisting that Person A is scientifically illiterate because of an extremely rare exception to the rule is ignoring statistics–statistically, the child is more likely to be not biological than to have an extremely rare variant. Statistically, men and women are far more likely to match in gender and sex than to not.

Let’s look at immigration, another topic near and dear to everyone’s hearts. After Trump’s comments about Haiti came out (and let’s be honest, Haiti’s capital, Port au Prince, is one of the world’s largest cities without a functioning sewer system, so “shithole” is actually true,) people began popping up with statements like “I’d rather a Ugandan immigrant who believes in American values than a socialist Norwegian.”

I, too, would rather a Ugandan with American values than a socialist Norwegian. However, what percentage of Ugandans actually have American values? Just a wild guess, but I suspect most Ugandans have Ugandan values. Most Ugandans probably think Ugandan culture is pretty nice and that Ugandan norms and values are the right ones to have, otherwise they wouldn’t have different values and we’d call those Ugandan values.

Updated values chart!

While we’re at it, I suspect most Chinese people have Chinese values, most Australians have Australian values, most Brazilians hold Brazilian values, and most people from Vatican City have Catholic values.

I don’t support blindly taking people from any country, because some people are violent criminals just trying to escape conviction. But some countries are clearly closer to each other, culturally, than others, and thus have a larger pool of people who hold each other’s values.

(Even when people hold very different values, some values conflict more than others.)

To be clear: I’ve been picking on one side, but I’m sure both sides do this.

What’s the point? None of this is very complicated. Most people can figure out if a person they have just met is male or female instantly and without fail. It takes a very smart person to get confused by a few extremely rare exceptions into thinking that the broad categories don’t functionally exist.

Sometimes this obfuscation is compulsive–the person just wants to show how smart they are, or maybe everyone around them is saying it so they start repeating it–but since most people seem capable of understanding probabilities in everyday life (“Sometimes the stoplight is glitched but usually it isn’t, so I’ll assume the stoplight is functioning properly and obey it,”) if someone suddenly seems incapable of distinguishing between extremely rare and extremely common events in the political realm, then they are doing so on purpose or suffering severe cognitive dissonance.

 

*Oddly, I solved the problem by giving the kids harder problems. It appears that when their brains are actively engaged with trying to solve the problem, they don’t have time/energy left to come up with alternatives. When the material is too easy (or, perhaps, way too hard) they start trying to get creative to make things more interesting.

 

North Africa in Genetics and History

detailed map of African and Middle Eastern ethnicities in Haaks et al’s dataset

North Africa is an often misunderstood region in human genetics. Since it is in Africa, people often assume that it contains the same variety of people referenced in terms like “African Americans,” “black Africans,” or even just “Africans.” In reality, the African content contains members of all three of the great human clades–Sub-Saharan Africans in the south, Polynesians (Asian clade) in Madagascar, and Caucasians in the north.

The North African Middle Stone Age and its place in recent human evolution provides an overview of the first 275,000 years of humanity’s history in the region(300,000-25,000 years ago, more or less), including the development of symbolic culture and early human dispersal. Unfortunately the paper is paywalled.

Throughout most of human history, the Sahara–not the Mediterranean or Red seas–has been the biggest local impediment to human migration–thus North Africans are much closer, genetically, to their neighbors in Europe and the Middle East than their neighbors across the desert (and before the domestication of the camel, about 3,000 years ago, the Sahara was even harder to cross.)

But from time to time, global weather patterns change and the Sahara becomes a garden: the Green Sahara. The last time we had a Green Sahara was about 9-7,000 years ago; during this time, people lived, hunted, fished, herded and perhaps farmed throughout areas that are today nearly uninhabited wastes.

The Peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages sheds light on how the Green (and subsequently brown) Sahara affected the spread (and separation) of African groups into northern and sub-Saharan:

In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. … We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase. …

Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.

In other words, modern North Africans have some maternal (female) Sub-Saharan DNA that arrived recently via the Islamic slave trade, but most of their Sub-Saharan Y-DNA (male) is much older, hailing from the last time the Sahara was easy to cross.

Note that not much DNA is shared across the Sahara:

After the African humid period, the climatic conditions became rapidly hyper-arid and the Green Sahara was replaced by the desert, which acted as a strong geographic barrier against human movements between northern and sub-Saharan Africa.

A consequence of this is that there is a strong differentiation in the Y chromosome haplogroup composition between the northern and sub-Saharan regions of the African continent. In the northern area, the predominant Y lineages are J-M267 and E-M81, with the former being linked to the Neolithic expansion in the Near East and the latter reaching frequencies as high as 80 % in some north-western populations as a consequence of a very recent local demographic expansion [810]. On the contrary, sub-Saharan Africa is characterised by a completely different genetic landscape, with lineages within E-M2 and haplogroup B comprising most of the Y chromosomes. In most regions of sub-Saharan Africa, the observed haplogroup distribution has been linked to the recent (~ 3 kya) demic diffusion of Bantu agriculturalists, which brought E-M2 sub-clades from central Africa to the East and to the South [1117]. On the contrary, the sub-Saharan distribution of B-M150 seems to have more ancient origins, since its internal lineages are present in both Bantu farmers and non-Bantu hunter-gatherers and coalesce long before the Bantu expansion [1820].

In spite of their genetic differentiation, however, northern and sub-Saharan Africa share at least four patrilineages at different frequencies, namely A3-M13, E-M2, E-M78 and R-V88.

A recent article in Nature, “Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81),” tells some of North Africa’s fascinating story:

Here, by using whole Y chromosome sequences, we intend to shed some light on the historical and demographic processes that modelled the genetic landscape of North Africa. Previous studies suggested that the strategic location of North Africa, separated from Europe by the Mediterranean Sea, from the rest of the African continent by the Sahara Desert and limited to the East by the Arabian Peninsula, has shaped the genetic complexity of current North Africans15,16,17. Early modern humans arrived in North Africa 190–140 kya (thousand years ago)18, and several cultures settled in the area before the Holocene. In fact, a previous study by Henn et al.19 identified a gradient of likely autochthonous North African ancestry, probably derived from an ancient “back-to-Africa” gene flow prior to the Holocene (12 kya). In historic times, North Africa has been populated successively by different groups, including Phoenicians, Romans, Vandals and Byzantines. The most important human settlement in North Africa was conducted by the Arabs by the end of the 7th century. Recent studies have demonstrated the complexity of human migrations in the area, resulting from an amalgam of ancestral components in North African groups15,20.

According to the article, E-M81 is dominant in Northwest Africa and absent almost everywhere else in the world.

The authors tested various men across north Africa in order to draw up a phylogenic tree of the branching of E-M183:

The distribution of each subhaplogroup within E-M183 can be observed in Table 1 and Fig. 2. Indeed, different populations present different subhaplogroup compositions. For example, whereas in Morocco almost all subhaplogorups are present, Western Sahara shows a very homogeneous pattern with only E-SM001 and E-Z5009 being represented. A similar picture to that of Western Sahara is shown by the Reguibates from Algeria, which contrast sharply with the Algerians from Oran, which showed a high diversity of haplogroups. It is also worth to notice that a slightly different pattern could be appreciated in coastal populations when compared with more inland territories (Western Sahara, Algerian Reguibates).

Overall, the authors found that the haplotypes were “strikingly similar” to each other and showed little geographic structure besides the coastal/inland differences:

As proposed by Larmuseau et al.25, the scenario that better explains Y-STR haplotype similarity within a particular haplogroup is a recent and rapid radiation of subhaplogroups. Although the dating of this lineage has been controversial, with dates proposed ranging from Paleolithic to Neolithic and to more recent times17,22,28, our results suggested that the origin of E-M183 is much more recent than was previously thought. … In addition to the recent radiation suggested by the high haplotype resemblance, the pattern showed by E-M183 imply that subhaplogroups originated within a relatively short time period, in a burst similar to those happening in many Y-chromosome haplogroups23.

In other words, someone went a-conquering.

Alternatively, given the high frequency of E-M183 in the Maghreb, a local origin of E-M183 in NW Africa could be envisaged, which would fit the clear pattern of longitudinal isolation by distance reported in genome-wide studies15,20. Moreover, the presence of autochthonous North African E-M81 lineages in the indigenous population of the Canary Islands, strongly points to North Africa as the most probable origin of the Guanche ancestors29. This, together with the fact that the oldest indigenous inviduals have been dated 2210 ± 60 ya, supports a local origin of E-M183 in NW Africa. Within this scenario, it is also worth to mention that the paternal lineage of an early Neolithic Moroccan individual appeared to be distantly related to the typically North African E-M81 haplogroup30, suggesting again a NW African origin of E-M183. A local origin of E-M183 in NW Africa > 2200 ya is supported by our TMRCA estimates, which can be taken as 2,000–3,000, depending on the data, methods, and mutation rates used.

However, the authors also note that they can’t rule out a Middle Eastern origin for the haplogroup since their study simply doesn’t include genomes from Middle Eastern individuals. They rule out a spread during the Neolithic expansion (too early) but not the Islamic expansion (“an extensive, male-biased Near Eastern admixture event is registered ~1300 ya, coincidental with the Arab expansion20.”) Alternatively, they suggest E-M183 might have expanded near the end of the third Punic War. Sure, Carthage (in Tunisia) was defeated by the Romans, but the era was otherwise one of great North African wealth and prosperity.

 

Interesting papers! My hat’s off to the authors. I hope you enjoyed them and get a chance to RTWT.