Three books to understand the “Dark Matter” of American History

Grand theories of history often have less utility than the claims they make for themselves. Marxism is a classic example.

But that does not mean that theories of history are useless. And arguably, Marxism is a classic example in this case too. Material forces and class conflicts can’t explain all of history, but they do explain some of history. Chris Wickham’s magisterial Framing the Early Middle Ages: Europe and the Mediterranean, 400-800 suffers from its excessive materialist and economistic thesis, but it also benefits from this perspective, because it captures part of the answer.

Moderation in all things, and due consideration to the importance of viewpoints in coloring perceptions, are the keys to comprehension in my opinion..

Today in some quarters it is fashionable to reduce all of history to the interplay between white supremacy and nonwhite peoples, who are depicted implicitly as nearly supine “noble savages,” existing in an Edenic state of nature before the intrusion of European peoples. This is a silly viewpoint from a scholarly perspective, and some of the ideological implications are ones which I object to most strongly.

And yet that begs the question, how does one understand the forces of history? In the American context, I think it is critical to understand the elementary regional folkways which congealed into these United States, and whose “cultural DNA” echoes down through the generations. Much of this is implicit and invisible culture because it is the culture of white English -speaking peoples of British provenance (though not all were Anglo, such as the French Canadians or Hispanos of the southwest).

Recently, Colin Woodward’s American Nations: A History of the Eleven Rival Regional Cultures of North America is the best example of this sort of work, which attempts to trace the historical dark matter the skeleton beneath the flesh. A more scholarly and narrow treatment can be found in David Hackett Fisher’s expansive Albion’s Seed: Four British Folkways in America. Finally, perhaps the most underrated and overlooked offering in this genre is Kevin Phillips’ The Cousins’ Wars: Religion, Politics, Civil Warfare, And The Triumph Of Anglo-America.

While Woodward focuses on all of North America, and Fisher more narrowly on the four folkways which extend from New England to the Deep South, Phillips’ integrates an American history with a broader narrative that shows the connections to events and processes occurring in the British Isles, and in particular England. The peculiarities of New England culture and economics, and their love-hate relationship to the British elites of the late 18th and 19th century, are critical pieces of the puzzle in explaining how the United States diverged from the United Kingdom, and, how the United Kingdom diverged from the United States.

If an understanding of population genetics allows one to decompose evolution and broadly biological phenomena into tractable analytic units, so an understanding of the elementary units of American culture, and their historical antecedents, shines a whole new light upon contemporary developments.

A genetic map of the world

The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow.  It is no great surprise that so many of the barriers correlate with rivers, mountains, and deserts. But the aim of this sort of work seems to be to make precise and quantitative intuitions which are normally expressed verbally.

To me, it is curious how the borders of the Peoples’ Republic of China is evident on this map (an artifact of sampling?). Additionally, one can see Weber’s line in Indonesia. There are the usual important caveats of sampling, and caution about interpreting present variation and dynamics back to the past. But I believe that these sorts of models and visualizations are important nulls against which we can judge perturbations.

As I said, these methods can confirm rigorously what is already clear intuitively. For example:

Several large-scale corridors are inferred that represent long-range genetic similarity, for example: India is connected by two corridors to Europe (a southern one through Anatolia and Persia ‘SC’, and
a northern one through the Eurasian Steppe ‘NC’)

We still don’t have enough ancient DNA to be totally sure, but it’s hard to ignore the likelihood that “Ancestral North Indians” (AN) actually represent two different migrations.

India also illustrates contingency of these barriers. Before the ANI migration, driven by the rise in agricultural lifestyles, there would likely have been a major trough of gene flow on India’s western border. In fact a deeper one than the one on the eastern border. And if the high genetic structure statistics from ancient DNA are further confirmed then the rate of gene flow was possibly much lower between demes in the past. Perhaps that would simply re-standardize equally so that the map itself would not be changed, but I suspect that we’d see many more “troughs” during the Pleistocene and early Holocene.

Because there are so many geographically distributed samples for humans, and frankly some of the best methods developers work with human data (thank you NIH), it is no surprise that our species would be mapped first. But I think some of the biggest insights may be with understanding the dynamics of gene flow of non-human species, and perhaps the nature and origin of speciation as it relates to isolation (or lack thereof).

My new podcast with Spencer Wells

Spencer Wells and I have a new podcast, The Insight. On the first episode, we’ll be talking about the Neolithic revolution.

We’ve already got several more in the pipeline that will come out in the next few weeks (being edited), including one with John Hawks. This will be a regular thing, so please subscribe!

Update: Also see:

Update: Here is the podcast embedded:

Helix kit price waived until December 26 at 2:59am EST

Happy Hanukkah! My main qualm with wishing you a happy holiday is that I’m a thorough assimilator and I don’t want to be disemboweled.

For the context, listen to the Stuff You Missed in History Class episode on the Maccabean Revolt. As a Jewish friend of mine once observed, the Maccabees were kind of the Al-Qaeda of their day (today she would have said ISIS).

With that out of the way, I want to give you a heads up that Helix has a sale going until December 26 at 2:59am EST where the $80 kit cost for purchase of any app is waived if you haven’t purchased at app before. Just enter the promotion code HOLIDAY at checkout.

That means presales of Insitome’s Regional Ancestry is no more than $19.99, while Neanderthal is $29.99 and Metabolism is $39.99 (this applies to all of Helix’s products except embodyDNA by Lose It! and Geno 2.0 by National Geographic).

Why does it matter? Again, Helix banks a high quality exome+ (the + is for non-exonic positions) when you purchase any of their apps. If you want subsequent apps you don’t have to sent another kit in, you just buy the app and get the results. Also, I do have to say that from what I’ve seen and heard Helix’s laboratory facilities are top-notch in terms of getting results turned around rapidly.

Your impatience is in your genes! (well, some of it)

Nature Neuroscience has a short communication which is very intriguging, Genome-wide association study of delay discounting in 23,217 adult research participants of European ancestry. How’d they get such a large sample size? Collaborating with our friends at 23andMe.

That being said, the abstract leaves a little to be desired:

Delay discounting (DD), the tendency to discount the value of delayed versus current rewards, is elevated in a constellation of diseases and behavioral conditions. We performed a genome-wide association study of DD using 23,127 research participants of European ancestry. The most significantly associated single-nucleotide polymorphism was rs6528024 (P = 2.40 × 10−8), which is located in an intron of the gene GPM6B. We also showed that 12% of the variance in DD was accounted for by genotype and that the genetic signature of DD overlapped with attention-deficit/hyperactivity disorder, schizophrenia, major depression, smoking, personality, cognition and body weight.

First, “Delay discounting (DD)”, is another way to say that you have high time preference. That is, you won’t forgo some gains in the short term for greater gains in the long term. You would really “fail” the marshmallow test.

Though there have been legitimate criticisms of the replicability of the effect size of the marshmallow test, there almost certainly is something to time preference and delayed gratification, and its relationship to the ability of young children to master the marshmallow test. In a macroeconomic sense societies characterized by low time preference can sustain lower interest rates, and lower interest rates have all sorts of stimulative properties on long-term economic growth.

But to be clear, the paper above does not detect a variant SNP, rs6528024, which explains 12% of the variance in DD. Rather, 12% of the variance could be accounted for by SNP-chip variance. That is, one could explain the “missing heritability” using the markers they had. The total heritablity of the trait is quite higher, 46% to 62% proportions are citied in the paper (narrow-sense). This means that of the total variance of the trait about half could be explained by additive genetic variance. Obviously the SNP-chip only captured a small minority of that additive genetic variance.

DD is correlated with a lot of things. There is a positive phenotypic correlation with:

  • Smoking
  • Substance abuse
  • Obesity
  • ADHD

They observed a positive genetic correlation between the variants associated with DD and:

  • Smoking
  • Neuroticism
  • Depression

And a negative genetic correlation with:

  • College completion
  • Years of education
  • Childhood IQ
  • Schizophrenia

In relation to the last, schizophrenia and DD are positively correlated phenotypically. That probably means that the underlying genetic causes of schizophrenia and DD are very different.

The patterns of correlations offer up a lot of avenues to speculate. They do a little of it in the paper, but are appropriately cautious. It seems entirely likely that in the near future we’ll be able to characterize a lot of the heriability genomically. When we figure out time preference and intelligence we’ll have come close to answering many of the questions that explain why different people have different life outcomes.

Note: It is no surprise that there is a negative correlation between DD (high time preference) and conscientiousness. Also, the association they found, GPM6B, has pretty clear biological relevance. It’s almost certainly real.

Endless Tigers Most Beautiful

The Thylacine, or the Tasmanian Tiger, is a tragic story that we all know (or should know!). Too late did humans realize how precious it was, a large(ish) marsupial carnivore endemic to Tasmania. Hunted to extinction, the last one died because it was not properly taken care of.

The Tasmanian Tiger is an example of why science is not just instrumental. That is, science is not simply the handmaid of engineering. Most people with an interest in biology have some instinctive reaction to the Tasmanian Tiger and what happened. There’s a natural pathos in it.

If you read The Monkey’s Voyage you know that the marsupials of South America probably derive from a single dispersal event. Genetics has determined that the South American Monito del monte is the most basal of the superorder Australidelphia, which includes all Australasian marsupials. That means instead of the single South American marsupial of this superorder being due to a migration from Australia, the Australian lineages diversified from a single South American ancestor. The Monito del monte is the last living descendent of this once extensive clade.

This means that all of the vareigated marsupials of Australia probably diversified during the Cenozoic, even though the divergence between marsupials and placental mammals dates deep into the Mesozoic. The Koala, the Kangaro, and the Tasmania Devil, all derive from the same source.

Well, a new paper in Nature: Ecology & Evolution does something quite neat, they sequence the whole genome of a Tasmanian Tiger! Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore:

The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.

The authors are saying that the clear morphological convergences between Tasmania Tigers and canids, which are obvious to anyone with eyes, aren’t detectable in similar sequence identity in regions of the genome known to be functional relevant to the characteristics of interest. Instead of sequence identity they suggest that rather the morphology is being controlled by evoutionary genetic process of cis-regulatory adaptation.

In the Mike Lynch vs. Sean Carroll debate of about ten years back, they’re saying that Sean Carroll was right (see this Hoekstra & Coyne paper for a different take).

Part of the issue here is probably the sort of traits they’re focused on. There seems to be something about the gross morphological characteristics humans find salient that make them the target of cis-regulatory mediated evolutionary processes.

Finally, they suggest with a PSMC plot that Tasmanian Tiger populations crashed around 70,000 years ago, well before Australian Aboriginals arrived. First, I’m not sure that I trust the 70,000 number to be precise enough that we can say it doesn’t overalp with human arrival. But second, is it me, or does every PSMC look like the pot above? It’s probably some sort of publication bias, as you don’t put in PSMC figures if they don’t show a bottleneck. But I’m kind of getting tired of it.

Open Thread, 12/11/2017

Thinking back to The Turks in World History the author points out that even the most explicit Islamic of the late Turkic empires, that of the Ottomans, persisted with a customary law similar and cognate to the Mongol yasa. Perhaps then the folkway of the nomadic Turk was sublimated and integrated into the Islamic superstructure of the Ottoman ruling ideology?

I went to a work-related Christmas party thrown by my company’s law firm. There were a lot of VC guys there. Two of them confused me for a blockchain entrepreneur (one of them was asking about a conflict with the CFO). I think I better get into blockchain….

So the website Everyday Feminism has an article, 10 Things Every Intersectional Feminist Should Ask On a First Date. I only know about this website because of conservative Twitter. It could be that 90% or more of the hits on this website are through viral “hate-clicks”.

Second, I feel the image that goes along with the article is problematic as fuck. The woman pictured seems to be geared toward appealing to cishet male norms of “attractiveness.” On the other hand, if intersectional feminists typically look something like Josie Maran…well, I won’t go there.

I will observe also that I find out about a lot of far-right movements and individuals through Left and Centrist Twitter (the two groups are interested for different reasons).

As noted in the comments, The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland. At this point, I think I can say this: unless it’s ancient DNA I’m done with the historical genetics of the British Isles. We know enough. Period.

Why the #MeToo Movement Should Be Ready for a Backlash. I don’t care too much about Al Franken, but digging a little deeper I think there might be some dirty tricks going on there…. I was rather dim on the prospects for Republicans in 2018, but at this rate, the Dems might “struggle-session” their way into defeat.

India Warily Eyes AI: Technology outsourcing has been India’s only reliable job creator in the past 30 years. Now artificial intelligence threatens to wipe out those gains. When I believed in the End of History and the Last Man this would matter to me. Now it’s all a big shrug.

The ancestral animal genetic toolkit revealed by diverse choanoflagellate transcriptomes.

Another reason that helper-AIs can’t come to medicine soon enough:

Chronicler of Islamic State ‘killing machine’ goes public.

As home DNA tests become more common, people must grapple with surprises about their parents:

Until recently, Andrea Ramirez, 43, thought she was part Mexican.

But the results from an at-home genetic test from 23andMe revealed that she is a mix of Northern European, North African and a little Native American.

And not at all hispanic.

There can be no genetic test for being Hispanic because that is a socio-cultural identity. There are Korean, Arab, and Nordic Hispanics. Even the most common genetic profile varies, from mostly European Argentines to mostly indigenous Bolivians to Afro-Cubans and Afro-Colombians.

When I read stuff like this I really wonder what they teach journalists (the Census explicitly declaims the the idea that Hispanic is a racial category).

I spent a fair amount of time this weekend cleaning up scripts that can batch process 23andMe, Ancestry and FamilyTree DNA input files and push them down the pipeline toward generating admixture percentages. I have posted the most current results from the South Asian Genotype Project have been posted.

Two things

1) I’m not happy with the clusters that I used. I may change them (in which case I’ll rerun everything).
2) Once I’ve done that I’ll probably send some of my scripts to Zack Ajmal and he can run all the Harappa individuals with this new cluster.

Finally, people from the “Cow Belt” don’t get genotyped. No submissions from UP or Bihar so far. Very frustrating.

The word problematic is problematic in my opinion. I really want to punch people when they use that word. But I’ve lost that battle.

My friend Chad Niederhuth is starting his plant genomics lab at Michigan State. He’s looking for graduate students and postdocs.

My friend Nathan Pearson’s HLA genomics start-up, Root is out of stealth mode.

Looking at my Kindle stack wondering about which of these five books to tackle next:

Why our society might go “splat!” on the windshield sooner than we think

Ray Kurzweil likes to talk about the fact that humans are bad at modeling exponential rates of growth. In this case, he’s talking about the rate of change in information technology. Whatever you think about Ray’s general ideas as outlined in books such as The Singularity Is Near, I think it’s a pretty good insight that needs reiteration.

More generally in social processes, I think humans living at any given time are not very cognizant of nonlinearities, and the sorts of exogenous shocks that might happen in their lifetimes. And why would we be? The evolutionary psychological model for why we’re bad at conceptualizing rapid change is that until recently not much changed for most people at most times.

That is, humans were animals which lived near the Malthusian limit at a stationary state. The rate of change did increase during the Holocene, but even with ancient Egypt consider how different the life of a peasant in the Old Kingdom was versus the New Kingdom. Over 2,000 years not much had changed. Even at the elite levels, not much had changed (in fact, the Egyptian religion maintained cultural continuity from ~3000 BC to ~500 AD, with the shutdown of the temple at Philae). Now consider the 2,000 years between ancient Rome and the modern West. Or, consider the 300 years between the Augustan Age and revival of the Empire under the Tetrarchy, and contrast that to the present year and 1717.

The modern world is strange because great changes in technology and social values can occur over and over across a single lifetime. Someone born in 1896 would mature and develop a world-view conditioned by the “long 19th century,” which lasted until 1914. Then they’d experience the “shock” of the “War to End All Wars.”

Arguably the period between the Congress of Vienna in 1815 and outbreak of World War I in Europe in 1914 was marked by evolution, rather than revolution, in social and political structures. 1848 did not prefigure a tumult equivalent to the French Revolution or the period of the Napoleonic Wars. Italy and Germany were unified ultimately under conservative nationalists. Darwinism, abolitionism, and women’s rights arguably were movements who were seeded during the Enlightenment and exhibited long pregnancies until the point that they erupted to prominence.

Between 1914 and 1920 a whole world fell away. The Empire of the Tsars collapsed, and was replaced by the chiliastic Bolshevik regime. Austria-Hungary and the Ottoman Empire were dismembered and their monarchies were overthrown, while Germany transformed from a conservative monarchy to a liberal republic.

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The Truth is that history is not evolving toward Truth

My friend Walter Olson pointed me to this from John Locke:

To love truth for truth’s sake is the principal part of human perfection in this world, and the seed-plot of all other virtues.

This is great and inspirational quote, but in most interpretive sieves I believe it is wrong. Hume’s assertion that “reason is and ought only to be the slave of the passions” is closer to the truth in terms of describing the typical human in terms of how they think, and what they value.

One of the insights of modern cognitive science is that the “rational” and “reflective” component of our mind tends to promote some delusions about its role in our decision-making process. Rather than being the conductor, it’s more often the rationalizer. That is, we make a decision, and then we concoct rationales after the fact. One can think of conscious rationality as a public relations outfit, as opposed to the client.

None of this is deep wisdom, and the latest research is all outlined in The Enigma of Reason. But, another issue which I think is important to note is that the propaganda over the generations by the very small proportion of the population for whom reason and truth are prioritized as the summum bonum of human existence, as implied by Locke’s assertion, have biased our understanding of history. The reason being that they are the ones disproportionately writing the history! Our species’ collective memory lies to us because cultural organs of memory have their own agendas (albeit, unconsciously!).

In Near Eastern antiquity the scribal caste was very much a group of literate wizards. No doubt some elements of literacy percolated to the general public, as is evident by graffito hieroglyphics by workers in ancient Egypt, but habitual engagement with the written word was the purview of a small group of professionals. These individuals dealt in abstraction in their day to day, and by the middle of the first millennium B.C. out of the culture of scribes developed the group we would term intellectuals. The philosophers, prophets, and sages of antiquity. A period when religion, magic, and science, were all one.

Of course, many of these intellectuals were not from the scribal caste as such. Many were aristocrats and gentry (e.g., Siddhartha and Plato). But by this time literacy had spread out beyond the scribal castes, and a civilian elite culture had emerged which valued intellectual pursuits in some fashion. Elite male leadership training in some societies began to include intellectual arts as part of their education. But we should be cautious about inferring from this that these elite males valued rhetoric and philosophy as ends in and of themselves. Rather, rhetoric and philosophy exhibited some instrumental (in politics for the former) and signaling value (abstruse philosophical abstraction could only be mastered by those with leisure and means, so it suggested one’s class origin and cultivation).

Across the centuries, and even millennia, the minority of intellectuals who notionally chased the truth, Plato, Sima Qian, and Ibn Khaldun, remain in our memories because their ideas were powerful, attractive, and their intellectual coherency and brilliance impressed future generations of thinkers. But we need not infer from this that in their own time they were of such inordinate fame or glory in relation to others of similar note though intellectual mediocrity. To give a concrete example, for a few shining decades phlogiston and Lysenkoism were bright and influential, even though the latter, and possibly the former, were both fraudulent enterprises.

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