In a bid to garner more visibility and support, researchers eager to sequence the genomes of all vertebrates today officially launched the Vertebrate Genomes Project (VGP), releasing 15 very high quality genomes of 14 species. But the group remains far short of raising the funds it will need to document the genomes of the estimated 66,000 vertebrates living on Earth.
The project, which has been underway for 3 years, is a revamp and renaming of an effort begun in 2009 called the Genome 10K Project (G10K), which aimed to decipher the genomes of 10,000 vertebrates. G10K produced about 100 genomes, but they were not very detailed, in part because of the cost of sequencing. Now, however, the cost of high-quality sequencing has dropped to less than $15,000 per billion DNA bases…
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Funding remains an obstacle. To date, the VGP has raised $2.5 million of the $6 million needed to sequence a representative species from each of the 260 major branches of the vertebrate family tree. To reach the goal of all 66,000 vertebrates will require about $600 million, Jarvis says.
Though a lot of the details are different (sequencing vs. genotyping, vertebrates vs. humans), many of the general issues that David Mittelman and I brought up in our Genome Biology comment, Consumer genomics will change your life, whether you get tested or not, apply. That is, to some extent this is an area of science where technology and economics are just as important as science in driving progress.
I remember back in graduate school that people were talking about sequencing hundreds of vertebrates. But even in the few years since then, the landscape has shifted. I’m so little a biologist that I actually didn’t know there were only~66,000 vertebrate species!
And yet this brings up a reasonable question from many scientists who came up in an era of more data scarcity: what are the questions we’re trying to answer here?
Challenges include justifying sequencing all these crappy genomes without research communities behind them https://t.co/HjpIlhXDSu
Science involves people. It’s not an abstraction. Throwing a whole lot of data out there does not mean that someone will be there to analyze it, or, that we’ll get interesting insights. To be frank, the original Human Genom Project project should probably tell us that, as its short-term benefits were clearly oversold.
In relation to how cheap data storage is and the declining price point of sequencing, I think my assertion that a genome, a sequence, is not a depreciating asset still holds. There is the initial cost of sequencing and assembling and the long term cost of storage, but these are small potatoes. The bigger considerations are the salaries of scientific labor and the opportunity costs. Sequencing tens of thousands of genomes may not get us anywhere, but really we’re not going to lose that much.
Ultimately I side with those who believe that the existence of the data itself will change the landscape of possible questions being asked, and therefore generate novel science. But it’s pretty incredible to even be debating this issue in 2018 of sequencing all vertebrates. That’s something to reflect on.
That sound you hear is the rumbling of the earth caused by the rippling tsunami that’s coming. The swell of ancient DNA papers focused on historical, rather than prehistorical, time periods. Some historians are cheering. Some are fearful. Others know not what to think. It will be. The illiterate barbarians of yore shall come out of the shadows.
If they had arrived on the edge of Europe two centuries earlier, the Avars would have a reputation as fearsome with the Huns, with whom they are often confused, and rightly so. But the Avars emerged as a force on the European landscape after the end of the West Roman Empire. The post-Roman polities did not have their own Ammianus Marcellinus (sorry Bede, you lived in the middle of nowhere).
And yet for centuries the Avars dominated east-central Europe and held the numerous Slavic tribes in thrall. They smashed past the borders of Byzantium during the reign of the heir of Justinian, and by 600 AD, on the eve of the great battle with Persia Constantinople had lost control of most of its Balkan hinterlands to these barbarians. A Byzantium which still controlled North Africa, much of Italy, southern Spain, Egypt, Anatolia, and the Levant, had been reduced to strongpoints all around the Balkan littoral. During the wars with the Sassanids, the Avars took advantage of the opportunity offered, and even raided the suburbs of Constantinople itself!
After 568 AD the nomadic Avars settled in the Carpathian Basin and founded their empire, which was an important force in Central Europe until the beginning of the 9th century AD. The Avar elite was probably of Inner Asian origin; its identification with the Rourans (who ruled the region of today’s Mongolia and North China in the 4th-6th centuries AD) is widely accepted in the historical research. Here, we study the whole mitochondrial genomes of twenty-three 7th century and two 8th century AD individuals from a well-characterised Avar elite group of burials excavated in Hungary. Most of them were buried with high value prestige artefacts and their skulls showed Mongoloid morphological traits. The majority (64%) of the studied samples’ mitochondrial DNA variability belongs to Asian haplogroups (C, D, F, M, R, Y and Z). This Avar elite group shows affinities to several ancient and modern Inner Asian populations. The genetic results verify the historical thesis on the Inner Asian origin of the Avar elite, as not only a military retinue consisting of armed men, but an endogamous group of families migrated. This correlates well with records on historical nomadic societies where maternal lineages were as important as paternal descent.
The samples were from a period about a century after the arrival of the Avars. It is not unreasonable to think that the Avar conquest meant that a continuous stream of Inner Asian pastoralists kept entering into the territory which they occupied for the opportunity, but this sort of genetic distinctiveness indicates that the Avars remained very separate from the people from whom they extracted tribute. Most, though not all, of these people, were or became Slavs.
Around 800 AD the Avars were finally defeated decisively by the Franks, and their elite converted to Christianity. I suspect this was the final step which would result in their assimilation over the next few centuries into the location population until they diminished and disappeared.
The results above support the proposition that the Pannonian Avars of the second half of the 6th century were the descendants of the Rouran Khaganate of the early half 6th century. The kicker is that the Rouran flourished in Mongolia! So like the Mongols six hundred years later, the Avars seem to have swept across the entire length of Eurasia that was accessible to their horses in a generation. To some extent, this is a recapitulation of the pattern we see nearly 3,000 years before the Avar, when the Afanasievo culture established itself in the Altai region, far from its clear point of origin in the forest-steppe of Eastern Europe.
Perhaps the period between 500 BC and 300 AD can be seen as an ephemeral transient between the vast periods before and after when pastoralists had free reign across most of temperate Eurasia?
A reader in the comments pointed me to Vice and Fire (though I’d already seen it on Twitter), a rumination on 20th century and 21st century fantasy literature by Peter Hitchens in First Things. Hitchens is the religious and politically conservative brother of the late Christopher Hitchens.
The piece is curious because it reflects more about Hitchens than the material which he is describing. First, he begins with perplexity that J. R. R. Tolkien’s secondary world seems to lack a moralistic high religion, as we’d understand it. To Hitchens this is confusing in light of the fact that Tolkien was a very religious Roman Catholic in his own life. But it isn’t as if Tolkien scholars haven’t noticed this juxtaposition, or the contrast with C. S. Lewis’s style, who was extremely heavy on Christian allegory.
I think the most plausible explanation is that Tolkien had something of the same issue as L. Sprague de Camp. An aeronautical engineer by training, Isaac Asimov in his autobiography In Memory Yet Green recounts that de Camp made the shift to explicit fantasy away from hard science fiction because his professional background made it difficult for him to engage in the suspension of disbelief necessary to write plausibly about faster-than-light travel and other such things. In fantasy his own background did not get in the way of his creativity.
Like de Camp, Tolkien was gifted with knowing too much. This was a man whose legendarium was an attempt to create for the English people a mythology similar to what the Scandinavians and Irish took for granted. A philologist who was a scholar of Beowulf, Tolkien knew the whole cultural corpus of the ancient pagan Germanic people well. He mined their mythos in constructing the world in which he set his fiction. As such, he was aware of the violent brutality which characterized pre-Christian, and frankly pre-civilized, Northern Europe, and how its folkways were at variance with Christian morality. If Tolkien applied his scholarly skills to creating religions for the Men of the West, it seems unlikely that he would have been comfortable sanitizing what he knew their practices would be. On the other hand, as an invented secondary world of the imagination, it was not plausible that they would be Christian, and in any case, Tolkien was a sincere and devout believer in the Christian religion and may have been uncomfortable mixing his imaginative fictional world with the metaphysical truths he held sacred.
And yet this does not mean that the ethical monotheism which J. R. R. Tolkien personally adhered to did not bleed into his work. In Return of the King, there is a well-noted reference to “heathen kings” and their practice of burning the dead. The Men of the West may not be Christians, but nor were they pagans.
Which brings me to Hitchen’s diatribe against George R. R. Martin’s attitude toward religion. Unlike Tolkien, Martin seems irreligious. Some fantasists, such a Anne McCAffrey and Ursula K. Le Guin, have created worlds where theism is understated or nonexistent (the Kargads in Earthsea do have something that we’d recognize as a religion grounded in gods…but they are the “bad guys”). Not so with Martin. His world exhibits a great deal of religious complexity and verisimilitude.
Perhaps too much verisimilitude for Peter Hitchen’s taste. Let me quote at length a description of the religions as from the piece above:
Some readers of Martin’s stories see a kind of Christianity in the worship of “the Seven.” This is the most official of several religions in Westeros, described in this way: “Worship was a septon [priest] with a censer, the smell of incense, a seven-sided crystal alive with light, voices raised in song.” There are a Father, a Mother, and a Smith. Then there are the Crone, the Maiden, the Warrior, and finally the Stranger, who represents death. Although the Seven faintly echo the Trinity, there seems to be no equivalent of Christ or the Holy Ghost among them, let alone of the One God. This is not Seven in One and One in Seven but Seven in Seven. I would say that the Seven are much more like classical or Nordic pantheons than like the Trinity…The worship of the Seven is exactly what atheists think Christianity is: an outward vesture.
A rival older faith, officially tolerated, survives in silent groves of ancient trees. There is also a rather nasty Drowned God, who seems to encourage piracy among seafarers (which suits them very well), and a highly intolerant Red God with a touch of the Cathars, but which (unlike the others) manifests itself in acts of violent wizardry and second sight. This is the deity that flourishes in the sweltering, cruel east, and no wonder. So we have on the one hand a vague expression of civic virtue, empty of real force and truth, and on the other a manifestation of supernatural might, quite unconnected with goodness and very ready to ally itself with earthly power if it suits them both. This recalls the way in which, in our time, science and power walk hand in hand, often destructively and dangerously.
This is where it strikes me that the author had a hammer, and everything was a nail. There’s some truth to what he’s saying. The religion of The Seven is never outlined in great detail in comparison to other quasi-medieval aspects of Martin’s world. But there is a backstory to this: apparently the religious institutions were subordinated and suppressed to some extent by the previous Targaryen dynasty (who were clearly only nominal converts in any case). The fact is that the Faith of the Seven is monotheistic, where each god is a manifestation of the single ultimate God. And, it is a religion derived ultimately from revelation to the Andals in Essos. This is not a naive and organic tribal paganism.
As for the religion of the Red God, Martin has admitted that its spread to Westeros is modeled explicitly on the spread of Christianity. It is intolerant, but so was the spread of the religion which Peter Hitchens is a personal devotee of. On the Isle of Wight the last pagans were mostly killed by invading Christians due to their reluctance to adopt the new religion. He claims to have read the books, but he gives no indication that the Red God is a favorite of the Brotherhood Without Banners, who fight to defend the common people against the depredations of warring lords. Though the Red Priest Melisandre commits evil, like those Protestants who burned witches in Northern Europe, she believes that any suffering is ultimately to further the good. The brutality of the followers of the Red God is the other face of the fact that they are zealous and on fire for their faith, and believers who have faith that they walk in the path of virtue. The Cathars who Hitchens allude to were persecuted and then slaughtered by the orthodox Christians.
What explains Hitchen’s bile then? I am being pedantic on the points he makes about Tolkien and Martin in part because not all readers of the above essay will have read the source material, and will take his misrepresentation at face value. But it is true George R. R. Martin’s worlds exhibit a high level of brutality and perversion. When I first read Martin’s work I just finished Bernard Cornwell’s Warlord Chronicles, which is a retelling of the Arthurian legend fixedly in post-Roman Dark Age Britain. I decided to email Martin to ask him if he was perhaps influenced by this work, and he did admit that he was a great admirer of the Warlord Chronicles. Martin has said repeatedly that his work attempts to show that just because someone takes a vow of knighthood does not necessarily entail that they are virtuous. As a point of fact many knights in the European Middle Ages were little better than mercenaries and brigands. Codes of conduct and broad ethical frameworks exist in part to tame, constraint, and smooth out the rough edges of military elites who rule by force of arms.
Additionally, like fantasist Robin Hobbs, Martin does not engage in plotting where your precious ones will always come out unscathed. This is a painful feature, not a bug. The idea is to humanize the protagonist, sometimes uncomfortably verging on creating anti-heroes, and to contrast the highs of the payoff with some major lows. The way Martin does this bothers many people, and I think it’s within their rights to be bothered. But for those of us who have read more anodyne and more juvenile fantasy works, encountering Martin’s work was a bracing shock and made us want more precisely because of the rougher texture and sharper edges.
Finally, there is one aspect where George R. R. Martin explicitly attempts to mimic J. R. R. Tolkien, and this is in creating a “low magic” world. More honestly, Martin’s magic is actually magic, rather than a different form of science and engineering. When Martin’s series began to gain prominence, fantasy had fallen into a period where formulaic magical elements resembling Dungeons and Dragons had saturated the genre, to the point where lazier authors often made recourse to magical deus ex machina. If you remember back to Tolkien you observe that there really wasn’t that much magic, and you never saw Gandalf cast spells like a carnival act.
Ultimately George R. R. Martin is attempting to pull off several things at once, and obviously he isn’t always doing it well, nor does he fulfill all the expectations of his readers. The broader framework of the world he is creating does exist in a sort of good vs. evil paradigm with dark magical forces. But Martin enjoys shades of gray, and coming from a background as a Hollywood screenwriter, he worked hard, perhaps too hard, to give his characters moral complexity. They are often both saints and sinners. Finally, though A Song of Ice and Fire is epic high fantasy, he has injected into its veins an element of dark historical fantasy. This does not not always work, and I suspect readers keying in on the high fantasy elements are easily repulsed by the frank brutality and amorality of the historical fantasy. To make an analogy, the flavors clash. Your mileage may vary on whether this is good or bad.
I personally get asked about the genetics of Afrikaners, because I’ve written about/analyzed the issue before. The main outlines seem to be established, but I thought I might go and revisit it again. The main reason is that we have ancient South African DNA, and I’ve been adding it to my personal analyses for a while. It might be worthwhile to reanalyze the South Africa samples I do have with some of these added in.
The plot at the top shows the core populations I started with. I did some outlier pruning. I only kept the South African samples that were overwhelmingly white. I picked Malays and a South Indian population because of Cape Coloureds, a mixed-race Afrikaans speaking group which has Asian ancestry that can be attributed to both South and Southeast Asian populations (the Dutch imported many slaves from India and had outposts in Java). I also used Bantu samples from South Africa, Kenya, as well as a Nigeria population. Finally, I also had some Hadza as a different hunter-gatherer population than the San Bushmen. For Europeans, I used white Dutch.
The final marker density as 200,000 SNPs, so not too bad.
As you can see if you click on the image all of the South African whites were shifted away from the Dutch. There were two outlier individuals, one of which was closer to the Dutch cluster, and one further. All the other individuals form a neat cluster. None of these individuals were close relatives.
Click to enlarge
I ran Treemix on the data with multiple migrations until the migrations stopped making sense to me. The African populations’ exhibit migration flows to each other. Much of it is entirely comprehensible. The Esan receive no migration, highlighting that this population did not receive gene flow from any groups in these data. The Kenya Bantus receive gene flow from the direction of Eurasians. This is also certainly Nilotic mediated. The gene flow they receive from the base of the ancient San is more enigmatic, but probably reflects uptake of local ancestry as the Bantus expanded. The southern Bantus receive gene flow from modern San.
The South African whites receive gene flow from a position on the graph between the modern San and other non-San African groups.
Click to enlarge
Next, I ran Admixture in the unsupervised mode with K = 6. The two populations mostly light-blue are South African whites and the Dutch, from the top to the bottom. You can see though that the South African whites clearly have other ancestral components. Most of these individuals have the components modal in the San, Esan Nigerians, Indians, and Malays. The two outlier individuals are also clear. The individual very close to the Dutch, but shifted toward the Asians, in the PCA does not have any African admixture. The individual shifted more toward the non-Europeans in the PCA also has more non-European fractions of ancestral components (that is, those components modal in non-European populations).
Next, I decided to confirm things by running a three population test. If you read this blog you’ve seen this before. Basically this is measuring shared ancestry by looking at deviations from a particular phylogenetic model: (test population(pop 1, pop2)). The relatedness of the test population to either pop1 or pop2 (that is, it’s a mix of the two) is measured by the negative f3 statistic, and I focused on z-scores greater than two.
Here they are:
Outgroup
Pop1
Pop2
f3
z
Bantu_NE
EsanNigeria
Dutch
-0.0009
-6.54
Bantu_NE
EsanNigeria
South_Africa_White
-0.0010
-6.54
Bantu_NE
EsanNigeria
Malay
-0.0009
-6.33
Bantu_NE
EsanNigeria
Telegu
-0.0008
-6.00
Bantu_NE
Bantu_S
South_Africa_White
-0.0008
-4.84
Bantu_NE
Bantu_S
Dutch
-0.0008
-4.77
Bantu_NE
Bantu_S
Malay
-0.0007
-4.21
Bantu_NE
Bantu_S
Telegu
-0.0007
-4.05
Bantu_NE
Dutch
San_Ancient
-0.0009
-3.02
Bantu_NE
Hadza
EsanNigeria
-0.0004
-2.97
Bantu_NE
Telegu
San_Ancient
-0.0007
-2.32
Bantu_NE
Malay
San_Ancient
-0.0007
-2.04
Bantu_S
EsanNigeria
San_Modern
-0.0028
-21.62
Bantu_S
EsanNigeria
San_Ancient
-0.0039
-20.78
Bantu_S
San_Ancient
Bantu_NE
-0.0030
-12.91
Bantu_S
San_Modern
Bantu_NE
-0.0019
-12.45
Bantu_S
Dutch
San_Ancient
-0.0031
-10.63
Bantu_S
Telegu
San_Ancient
-0.0030
-10.33
Bantu_S
San_Ancient
South_Africa_White
-0.0027
-9.17
Bantu_S
Malay
San_Ancient
-0.0029
-8.97
San_Modern
Dutch
San_Ancient
-0.0091
-34.96
San_Modern
Telegu
San_Ancient
-0.0087
-33.86
San_Modern
San_Ancient
South_Africa_White
-0.0089
-33.54
San_Modern
San_Ancient
Bantu_NE
-0.0063
-31.93
San_Modern
Malay
San_Ancient
-0.0085
-30.98
San_Modern
Bantu_S
San_Ancient
-0.0052
-28.91
San_Modern
Hadza
San_Ancient
-0.0051
-27.58
South_Africa_White
Dutch
Bantu_NE
-0.0017
-12.96
South_Africa_White
EsanNigeria
Dutch
-0.0017
-12.68
South_Africa_White
San_Modern
Dutch
-0.0018
-12.41
South_Africa_White
Bantu_S
Dutch
-0.0017
-12.36
South_Africa_White
Dutch
San_Ancient
-0.0021
-12.14
South_Africa_White
Hadza
Dutch
-0.0014
-10.41
South_Africa_White
Malay
Dutch
-0.0007
-5.97
South_Africa_White
Telegu
Dutch
-0.0003
-3.64
Telegu
Malay
Dutch
-0.0004
-2.79
No surprises so far. One thing that did surprise me though was the extent of the admixture even after PCA outlier removal. So I took the output you saw above and removed individuals that were very mixed, except for the case of the white South Africans. Then, I ran admixture in supervised mode, where the “pure” populations were fixed as references (I merged the moden San without much admixture with the ancient San). You can see the results below:
Click to enlarge
Re-running the three population test with these “pure” populations I only got significant results for the below cases:
Outgroup
Pop1
Pop2
f3
z
South_Africa_White
Dutch
EsanNigeria
-0.0017
-13.1937
South_Africa_White
San
Dutch
-0.0020
-12.6910
South_Africa_White
Hadza
Dutch
-0.0014
-9.7246
South_Africa_White
Malay
Dutch
-0.0009
-6.6481
South_Africa_White
Telegu
Dutch
-0.0004
-4.6167
No big surprise.
The average European ancestry I got in my South African white samples, N = 12, is 93.5%. Making a composite individual, note that if someone had great-great-grandparents who were not European, they would be expected to have 6.25% non-European ancestry. That’s 4 generations back. So about 100 years. These individuals are presumably adults. Let’s say they are 25 years old. That goes back 125 years. It’s probably reasonable in a single person admixture people to suggest it was sometime in the mid to late 19th century.
This seems unlikely. The evenness of admixture and balance between different groups indicates that it is older than that, and they are obtaining it from different lineages. Traditional genealogical estimates suggested in the range of 5-7.5% non-European ancestry in Afrikaners, and one study of 185 individuals showed 18% non-European mtDNA.
I will probably do some ancestry deconvolution and see if I can get a figure for the time of admixture (though the fractions here are very small, as is the sample size of the admixtured population). But the non-European ancestry of Afrikaners is uncannily similar to the non-European ancestry of the Cape Coloureds. That to me leads us to the conclusion that in the early European settler community a fair number of mixed-race women married in. Those mixed-race women who married mixed-race men helped found the Cape Coloureds.
On the most general level, the spread of these obvious fakes is a matter of the epidemiology of ideas. Basically, the ubiquity of these fakes is like the spread of chain letters or viruses which hack our cognitive biases. By analogy, consider the fondness for Qing China exhibited by some early modern European thinkers, such as Leibniz and Voltaire. With hindsight, it is clear that their affection for Chinese civilization was a reflection more upon their critique and aspiration of their own civilization. For Leibniz, bureaucratic rationalism, and Voltaire, secular humanism.
Centuries on their Sinophilia is of academic interest as a fragment of cultural history which brings into salience particular currents which bubbled up during the period of both European modernization and development vis-a-vis the rest of the world, and the last contact that European civilization made with a powerful and self-assured alien civilization, that of China under the Kangxi Emperor, Yongzheng Emperor, and Qianlong Emperor. If you want to understand China during this period, its culture and politics, then these early modern thinkers are not the ones to consult. Their opinions and views on China shed more light on currents in their own culture than the reality in China.
A similar thing happened to Islam and Islamic civilization after the 18th century. As Western civilization was secularizing some intellectuals pointed to the world of Islam as evidence that some tolerance of pluralism would be sustainable and preferable. What is being alluded to here is the system of formalized tolerance of the “People of the Book”, dhimmis, within Islam from its earliest period. But the highlighting of the Muslim alternative was less about Muslims and more about the reality of a post-Reformation early modern Europe riven by sectarian pluralism, as well as incipient secularization of a substantial numbers of intellectuals who began to perceive themselves as dissenters from the regnant orthodoxy as a class.
There is a scholarly study that engages in the exploration of the development and crystallization of the Muslim system of tolerance of religious minorities. That scholarship plumbs into the depths of the early formalization of Islam as a distinctive confession and civilization, and its roots (including the tolerance of dhimmis) in Byzantine and Sassanian practice. But when most people speak of the tolerance of early Islam in the West, they are speaking about and engaging issues related to the West, not Islam, which is simply a tool or instrument in an argument particular to factions within the West.
Going back to this specific issue, the fabrication of the depiction of “Islamic science,” there is a particular social and cultural context in the West that needs to be highlighted (as opposed to the Muslim world, which is a somewhat different dynamic, and analogous to the rise of Vedic science). Early modern secular intellectuals who contrasted the intolerance of Christian civilization to the relative tolerance of Islamic civilization were working implicitly within a modernist framework where objective truth would eventually pave the way for a universal civilization which would evolve out of the post-Christian West. This attitude is exemplified by the liberal French nobleman, Stanislas Marie Adélaïde, comte de Clermont-Tonnerre, who when arguing for removing various restrictions on Jews declared “We must refuse everything to the Jews as a nation and accord everything to Jews as individuals.”
These modernist conceits of clear and distinct universal truths and moralities leading to a common human ethos have fallen by the wayside. Rather, today many who espouse multiculturalist viewpoints are careful not to aver that one culture is superior or more advanced than another. This assumption means that today many reject a progressive and Whiggish view of history which implicitly highlights Western exceptionalism between 1700 and the current age.
These people may not be comfortable with the assertion that the form of intellectual inquiry that emerged out of Renaissance natural philosophy that we today call science is sui generis. A particular expression of the genius of Western civilization. Rather, what it is appealing toward many with a multiculturalist viewpoint, where all cultures have notionally similar ethical values, is that all cultures produce their own form of science, just as valuable, exceptional, and illustrative of universal human genius.
With Islam and science anyone with superficial interest in the topic can be easily convinced of the genius of individuals such as Ibn Sina. If the the great Bukharan polymath had been born today it would not be surprising if perhaps he became a scholar of some renown. But the reality is that most of the people who will tell you that Islam once had great scientists could not name a single scientist of pre-modern Islam. Just as with Voltaire and the Chinese, modern Western intellectuals who have moved beyond Whiggishness and naive modernism see in other cultures something that serves to critique and comment on their own. The legend of Islamic science is an instrument, a tool, in a particular deconstruction of the “myth” of Western science.
A curious aspect of this viewpoint, which is in some ways highly relativistic in relation to epistemology (“other ways of knowing”), is that it is also highly universalistic in ethics. Other cultures are shoehorned into frameworks and paradigms of Western making, particular mirrors through which all are seen darkly.
This is the same observation that could be made of early modern Whiggishness, where all cultures are seen as ascending slowly up a ladder of complexity and progress, with Northwest Europe in particular leading the way. Whigs viewed history in a linear fashion, and all societies could be placed along the sequence.
So what’s the multiculturalist/progressive/post-modern analog? It is common today in progressive Western circles to strive toward radical gender, sexual, and ethnoreligious egalitarianism. Justice. Many a time I have seen that patriarchy or sexual traditionalism are presumed to be colonial (white, Western) impositions on other societies. Western Muslims of a progressive bent may even assert that Islam is fundamentally and originally feminist and egalitarian. Hindu progressives likewise may highlight the depictions of sex acts Khajuraho temple complex as indicative of a liberal and tolerant attitude toward these matters before the arrival of the British, who introduced conservative bourgeois morals (note that often the terminology itself points to the operation of these individuals in a very Western tradition).
Nearly two hundred years ago the British Whigh politician Thomas Macaulay declared:
“We must at present do our best to form a class who may be interpreters between us and the millions whom we govern; a class of persons, Indian in blood and colour, but English in taste, in opinions, in morals, and in intellect. To that class we may leave it to refine the vernacular dialects of the country, to enrich those dialects with terms of science borrowed from the Western nomenclature, and to render them by degrees fit vehicles for conveying knowledge to the great mass of the population.”
Today progressive Westerners would never say such a thing. In part, because they would never assert that the West, and its culture, was in any way superior to that of the non-West. On the contrary, the tacit assumption might be that it was the West which manufactured and perfected the modes of oppression which spread across the world and caused human misery. With decolonization and the recession of Western imperialism, one would then see a diminishment of oppression and presumably human misery.
The difference between a 19th century liberal such as Thomas Macaulay is that whereas he perceived that the Indians would have to change their morals and develop their intellects to ever be equal to the English, today his progressive counterpart fundamentally assumes that the natural state of humanity was one of moral and intellectual equivalence. That is, oppression, the subjugation of women and minorities, the “marginalized”, was invented by Western Europeans, and imposed on non-Europeans. It is Western colonialists who brought the sin of oppression into the garden. They were responsible for the fall from ethical perfection, the stage of original grace.
Non-Europeans do differ from Europeans, but only in matters of detail, outward dress, food, and architecture. Accidents. But in matters of essence, there is no difference at all.
This conceit leads to all sorts of confusions.
After purchasing his papers, John Maynard Keynes declared Isaac Newton “was the last of the magicians, the last of the Babylonians and Sumerians.” One can not deny that Isaac Newton was a genius, invariant of the age. Nor can one deny his scientific contributions, which modern undergraduates doing any scientific course of study must master to some extent. But the world of Isaac Newton was a different world, where witches were still burned, and men and women in the British Isles could still be executed for atheism. People did science, but not quite in the modern way. People were religious, but not quite in the modern way. There is a gap between 1700 and 2000.
Similarly, the ancient Greeks did science. But it was different from modern science, which is contingent on a sequence of events which are rooted in the latter Rennaissance. Did the Muslims of the “Islamic Golden Age” do science? I would say so. But like the Greeks, it was different from what came later (one could say the same of the “Aristotelian Renaissance”).
One must take the history of different cultures on their own terms, and understand them in the broad scope of human history. Theories are useful, but only in concert with a genuine engagement of the empirical record. Whigs and Marxists had theories, which grasped at essential fragments of reality but often obscured critical detail. There is a particular type of fashionable intellectual today who claims to eschew theory and focus on “thick description,” who nevertheless sneaks a particular theory of history through the back door, a variant of the “Noble Savage.”
In particular relation to “Islamic science,” there is some interesting detail in the texture of reality that is exposed when we attempt to understand it on its own terms. One thing which jumps out at you is that since most people are not particularly interested in the details, the terminology you use matters a great deal. Usually, we are focusing on the period between 750 A.D. and sometime around 1000 A.D. Now, when you use the term “Islamic Golden Age” or “Islamic science,” you obscure the reality that many prominent intellectuals during this period were not Muslim.
For example, Thabit ibn Qurra was a Sabian, which referred to the pre-Islamic and pre-Christian inhabitants of the city of Harran. The natives of Harran seem to have preserved religious traditions from Mesopotamian antiquity, in particular, astral cults. Additionally, they were also preservers and connoisseurs of Greek philosophical thought.
Though Sabians were exotic, Christians were dominant features of the scene during the early years of Islam and were instrumental in translation and preservation. In the Aeon piece, the author suggests that it should be called “Arab science” as opposed to “Islamic science.” But among the Muslims, most of the great thinkers were Iranians. That is Persians, or from related peoples. It is true that they wrote in Arabic, but Arabs were only a minority of the subjects of the Arab Caliphates before 1000 A.D. One reason Al-Kindi is exceptional is he was an Arab of the Arabs. A scion of an Arab tribe, with a lineage rooted in that ethnicity before Islam.
Matthew Cobb, an evolutionary biologist, uses the term “Arabic science” in his work to avoid these confusions. This reflects the fact that Arabic was the medium of communication between these scholars, irrespective of religion and ethnicity. In this way, it’s analogous to “Latin science,” which is probably a good term for the intellectual tradition which flourished in Western European during the Aristotelian Renaissance, and later on into the early modern period.
The universal moral of the story is that understanding history, and intellectual history, in particular, is hard. One must balance between commensurable universality and startlingly different local particularity. What is easy is co-opting and hijacking the shape of reality for one’s own ideological preferences. Humans are natural system-builders, theoretical thinkers. The reason being that systems allow one to come to conclusions without doing much research. Logical inference from presuppositions takes more mental effort than an intuitive reflex. But, it takes far less effort that researching the abyss of data from which one can make robust and genuine inferences, and test one’s theoretical reflexes.
But that journey is rewarding. Because it leads to understanding other peoples as ends unto themselves, rather than instruments.
Ancient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, migration, and admixture events for extinct taxa. Outside the permafrost, however, irreversible aDNA post-mortem degradation has so far limited aDNA recovery within the ~0.5 million years (Ma) time range. Tandem mass spectrometry (MS)-based collagen type I (COL1) sequencing provides direct access to older genetic information, though with limited phylogenetic use. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae using ~1.77 million years (Ma) old dental enamel proteome sequences of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus). Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that this genus includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference, and also provides additional information about the sex and the taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.
Dmanisi. If that doesn’t mean something, look it up!
Zha pointed me to this report, Massive Numbers of Uyghurs & Other Ethnic Minorities Forced into Re-education Programs, which is the source for the number in articles like this: U.N. Panel Confronts China Over Reports That It Holds a Million Uighurs in Camps. It’s short, but if you don’t want to read, there are major reasons to be skeptical of the 1 million figure as being credible. I think it’s likely that the Chinese government is targeting Uyghurs for re-education, partly because there’s a long history of that sort of thing. But the Kashgar region, in particular, strikes me as extremely unrepresentative, due its particular nature (far more Uyghur and Muslim than any other area of China).
A certainly number of professors have, are, and will, engage in sexually inappropriate relationships with their graduate students. Ronell seems likely to be in that class, but the more interesting aspects are of the story are:
1) That prominent fashionable professors, such as Zizek and Judith Butler have defended her (Butler had a follow-up equivocation, but who knows, perhaps it’s just performative).
2) Ronell is a certain type of academic who everyone who has been in academia has heard of or experienced. The depiction in the Salon story makes her seem like a total psychopath who suborns the mission of the institution toward the service of her self-aggrandizement. This is a certain type of professor. A certain type of business person. A certain type of middle manager. We all know of these people. It’s not surprising that they exist in the academy. But, I do wonder if the transparent fixation on style above substance in the field of scholarship, “deconstruction”, that Ronell operates within allowed her selfish and narcissistic tendencies to flourish in a manner it wouldn’t have if she was engaging in supervising laboratory work or archival research.
The Iberian Peninsula, lying on the southwestern corner of Europe, provides an excellent opportunity to assess the final impact of population movements entering the continent from the east and to study prehistoric and historic connections with North Africa. Previous studies have addressed the population history of Iberia using ancient genomes, but the final steps leading to the formation of the modern Iberian gene pool during the last 4000 years remain largely unexplored. Here we report genome-wide data from 153 ancient individuals from Iberia, more than doubling the number of available genomes from this region and providing the most comprehensive genetic transect of any region in the world during the last 8000 years. We find that Mesolithic hunter-gatherers dated to the last centuries before the arrival of farmers showed an increased genetic affinity to central European hunter-gatherers, as compared to earlier individuals. During the third millennium BCE, Iberia received newcomers from south and north. The presence of one individual with a North African origin in central Iberia demonstrates early sporadic contacts across the strait of Gibraltar. Beginning ~2500 BCE, the arrival of individuals with steppe-related ancestry had a rapid and widespread genetic impact, with Bronze Age populations deriving ~40% of their autosomal ancestry and 100% of their Y-chromosomes from these migrants. During the later Iron Age, the first genome-wide data from ancient non-Indo-European speakers showed that they were similar to contemporaneous Indo-European speakers and derived most of their ancestry from the earlier Bronze Age substratum. With the exception of Basques, who remain broadly similar to Iron Age populations, during the last 2500 years Iberian populations were affected by additional gene-flow from the Central/Eastern Mediterranean region, probably associated to the Roman conquest, and from North Africa during the Moorish conquest but also in earlier periods, probably related to the Phoenician-Punic colonization of Southern Iberia.
The Insight will be putting up a podcast on the life and science of L. L. Cavalli-Sforza. Spencer worked with Cavalli-Sforza as a postdoc at Stanford in the late 1990s.
A recommendation from The Scholar’s Stage has finally pushed me to complete Imperial China 900–1800, a book which I first began reading over ten years ago. Like The Fall of Rome: And the End of Civilization this may be a work I read again and again. Unlike The Fall of RomeImperial China is not tightly argued. There is no argument, just narrative and exposition. It is not a short treatise purporting to “explain,” it is a magnum opus “describing” (in this it is similar to A History of Byzantine State and Society). The author, F. W. Mole, is clearly a scholar of deep learning. He doesn’t “front” with puffy theory and lexical flourish. He knows things. Many things. Imperial China was the summation of his learning. Decades of the accretion of insights.
Because I have read a fair amount of Chinese history reading Imperial China has illuminated some phenomena that had earlier eluded me in terms of their causal roots. During the Tang dynasty, and again during the Yuan (Mongol) period, people of Central Asian provenance had a despised but critical role in Chinese society. During the Tang period, Central Asian Sogdians were renowned and reviled as money-lenders and merchants. During the Yuan period, Central Asians were administrative bureaucrats who dominated the civilian officialdom of the Chinese state (this, due to Mongol favoritism in a land where the Han were a recently conquered overwhelming majority).
This is a deviation from the norm in Chinese history. Civilian rule in China was often delegated to learned scholars, usually stepped in Confucian classics. The trend began during the Han dynasty. During the Sui-Tang dynasty, the prominence of aristocratic factions attenuated the role of gentry officials, but the arc of history bent toward meritocracy, and so it revived with much greater vigor during the Song dynasty.
Motte notes that one reason the Central Asians may have been reviled so is that they practiced a West Asian tradition of revenue extraction which was at variance with Chinese norms. Basically, the Central Asians were “tax farming.” In ancient Rome, this practice was severely criticized. The contrast here is with a long and robust tradition within orthodox Confucianism that the role of the state and the official class was to foster prosperity by minimizing tax burdens on the populace, not extract resources for their own enrichment. Obviously the Chinese have a long history of corruption, self-dealing, and the emergence of local petty tyrants. But the ideal, and a repeated trend in behavior among many scholar-officials across history is toward service to the state in the interests of the collective well-being and as well as the extolling of individual virtue. Glory did not go to god or the state, but the people.
This is why I have joked that Confucianism really pioneered Fusionism 2,000 years ago.
Though drawing straight-line inferences from history is a fool’s game, I have started to wonder if China’s timeless absorptive capacity due to its resilience and continuity can tell us something about its trajectory in the 21st century. I am well aware of the reality that demographics are not on its side (China’s working age population is shrinking). Ignoring this for a moment, let us take seriously the proposition that China is fundamentally bound together by something culturally ineffable, and deeply reflects the Confucian mores that have waxed and waned for 2,000 years. To not put too fine a point on it many perceive, correctly, an amoral rapacity in the modern quasi-Communist Chinese people. Some of my friends are not very optimistic about the Chinese, after having worked with them in a professional capacity. They find both their proximate moral character and ultimate vision lacking.
And yet for thousands of years, the Chinese maintained a cultural and civilizational identity which was extremely robust. When introduced to the foreign religion of Buddhism, China made it its own. In fact, Buddhist concepts and institutional structures reshaped religious Daoism. Cults like Christianity, Islam, and Manichaeanism have all entered China, and been transmuted, or appropriated. There is obviously a Chinese sense of self that is rooted in history, in cultural memory, but oftentimes these ethnocultural entities also transmit tacit and informal folkways.
It is certainly true that the scholar-officials of the Chinese bureaucratic class were not always well prepared for some of the exigencies which they were confronted with. Brittle, often hidebound, bureaucrats were often stuck at a “local optimum.” But over the long-term historically they have adapted, integrating some of the metaphysical insights of Buddhism into Neo-Confucianism most prominently, as well as adapting the Chinese imperial system to an explicitly and self-consciously non-Han ruling caste such as the Manchus.
Social disorder in China historically can have tragic consequences. The Taiping Rebellion in the 19th century resulted in the death of tens of millions. And yet China has persisted for 2,000 years as a unitary state, on and off. Its cultural and social fiber has roots into a deeper past, during the declining years of the Zhou during the first millennium before the birth of Christ. What Imperial China illustrates is that Chinese civilization had particular and locally contingent resources which allowed for the flourishing of a relatively well-ordered administrative state less contingent on tribal asabbiya necessary in West Asian polities.
In short, if “Confucian civilization” is a thing, I’m somewhat more optimistic about 25% of our species over the next few decades.
Since the death of L. L. Cavalli-Sforza I’ve been thinking about the great scientists who have passed on. Last fall, I mentioned that Mel Green had died. There was a marginal personal connection there. I had the privilege to talk to Green at length about sundry issues, often nonscientific. He was someone who been doing science so long he had talked to Charles Davenport in the flesh (he was not complimentary of Davenport’s understanding of Mendelian principles). It was like engaging with a history book!
A few months before I emailed Cavalli-Sforza, I had sent a message on a lark to James F. Crow. It was really a rather random thing, I never thought that Crow would respond. But in fact he emailed me right back! And he answered 10 questions from me, as you can see below the fold. The truth is I probably wouldn’t have thought to try and get in touch with Cavalli-Sforza if it hadn’t been so easy with Crow.
If you are involved in population genetics you know who Crow is. No introduction needed. Some of the people he supervised, such as Joe Felsenstein, have gone on to transform evolutionary biology in their own turn.
Born in 1916, Crow’s scientific career spanned the emergence of population genetics as a mature field, to the discovery of the importance of DNA, to molecular evolution & genomics. He had a long collaboration with Motoo Kimura, the Japanese geneticist instrumental in pushing forward the development of “neutral theory.”
Below are the questions I asked 12 years ago. My interests have changed somewhat, so it’s interesting to see what I was curious about back then. And of course fascinating to read Crow’s responses. Read More
The late Gordon R. Dickson wrote a series of books in a (mostly) future history termed The Childe Cycle. I’ve read a substantial number of the books in this series, and it’s rather uneven. On the whole, I would say that the earlier books are better than the later works. Dickson died before he could complete the series, but I don’t think that’s really that big of a deal, because the books are only loosely connected. I read the novels and short stories of the series all out of order, and it wasn’t a problem.
One of the interesting aspects of the universe is that there are separate human cultures/ethnicities that inhabit different planets and specialize in different economic tasks. If you look closely, the system doesn’t make economic sense, but that’s OK, we’re talking a setting for space opera.
Of the “splinter cultures,” two of them inhabit planets very close to each other in the same solar system, Newton and Cassida. Newton is home to pure scientists, while Cassida is a world of applied engineers. In Young Bleys it is stated that the engineers of Cassida admire and envy the scientists of Newton.
My point in posting about this is to a great extent I imagine that the United States of America will be the “Newton” of our world for a while longer. But, other nations will be will Cassida (you can guess which), and others the Friendlies. I don’t know who the Exotics or Dorsai might be, and the analogy might breakdown there.