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	<title>Razib Khan, Author at Palladium</title>
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	<title>Razib Khan, Author at Palladium</title>
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		<title>As Caste Vanishes Only Genes Remain
</title>
		<link>https://www.palladiummag.com/2024/04/05/as-caste-vanishes-only-genes-remain/</link>
		
		<dc:creator><![CDATA[Razib Khan]]></dc:creator>
		<pubDate>Fri, 05 Apr 2024 13:00:55 +0000</pubDate>
				<category><![CDATA[Articles]]></category>
		<guid isPermaLink="false">https://www.palladiummag.com/?p=7063</guid>

					<description><![CDATA[<p>As Indian Americans continue their socioeconomic ascent, the relevance of caste evaporates. Yet researchers have found evidence this social technology was sustained for thousands of years.</p>
The post <a href="https://www.palladiummag.com/2024/04/05/as-caste-vanishes-only-genes-remain/">As Caste Vanishes Only Genes Remain
</a> appeared first on <a href="https://www.palladiummag.com/">Palladium</a>.]]></description>
										<content:encoded><![CDATA[<div>
<p><i>This article by Razib Khan will feature in PALLADIUM 18: Biological Inheritance, our 2025 summer print edition. <a href="https://buy.stripe.com/aEU2b7aHCdBgdck8wH">Subscribe now</a> to receive your copy.</i></p>
</div>
<p data-pm-slice="1 1 []">In February 2022, Seattle became the <a href="https://www.npr.org/2023/02/22/1158687243/seattle-becomes-the-first-u-s-city-to-ban-caste-discrimination" target="_blank" rel="noopener noreferrer nofollow">first U.S. city to ban</a> caste-based discrimination. This follows the California State University student body association banning caste-based discrimination, in addition to the University of California, Davis and Brown University. In 2020, a <a href="https://news.bloomberglaw.com/daily-labor-report/rare-caste-bias-case-advances-raising-calls-for-federal-action" target="_blank" rel="noopener noreferrer nofollow">lawsuit</a> was filed in California against Cisco Systems alleging caste-based discrimination where a lower-caste Dalit employee was passed over for promotion by an upper-caste Brahmin colleague. The case against two individuals accused of discrimination was dismissed, but the suit against Cisco continues to be litigated. What’s going on here?</p>
<p>There are three intersecting factors at play in modern American society that make caste relevant. First, Indian Americans are now publicly prominent. Long the most educated and wealthiest ethnic group in the U.S., they have become prominent in politics and business in the past few decades. Not only are the CEOs of Google, Microsoft, and Starbucks Indian American, but two Republican candidates for the presidential nomination—Vivek Ramaswamy and Nikki Haley—were Indian American, while the current Vice President, Kamala Harris, is the daughter of an Indian woman. They are now the quintessential visible minority at the commanding heights of American culture.</p>
<p>Second, the caste system is inextricably linked to Indian, and more precisely Hindu, identity in the minds of most Americans. In fact, most elementary school treatments of Indian history and society include a section on caste. And third, the hierarchical caste system is a perfect foil for the current American elite’s fixation on social panics and policies targeted at grades of status. India’s caste system is the absolute inversion of the egalitarian and flat utopia envisioned by modern social justice acolytes—though ironically, both are highly identitarian.</p>
<p>Though the caste system dominates much of Indian life, it does not dominate Indian American life. At slightly over 1% of the U.S. population, only about half of Indian Americans identify as Hindu, the religion from which the broader categories of caste, or <em>varna</em>, emerge. While caste endogamy—marrying within one’s caste—in India remains in the range of 90%, in the U.S. only 65% of American-born Indians even marry other people of subcontinental heritage, and of these, a quick inspection of <em>The New York Times </em>weddings pages shows that inter-caste marriages are the norm. While tensions between the upper-caste minority and middle and lower castes dominate Indian social and political life, 85% of Indian Americans are upper-caste, broadly defined, and only about 1% are truly lower-caste. Ultimately, the minor moral panic over caste discrimination among a small minority of Americans is more a function of our nation’s current neuroses than the reality of caste in the United States.</p>
<p>But this does not mean that caste is not an important phenomenon to understand. In various ways, caste impacts the lives of the more than 1.4 billion citizens of India—18% of humans alive today—whatever their religion. While the American system of racial slavery is four centuries old at most, India’s caste system was recorded by the Greek diplomat Megasthenes in 300 BC and is likely far more ancient, perhaps as old as the Indus Valley Civilization more than 4,000 years ago. Indian caste has a deep pedigree as a social technology, and it illustrates the outer boundary of our species’ ability to organize itself into interconnected but discrete subcultures. And unlike many social institutions, caste is imprinted in the very genes of Indians today.</p>
<h3><strong>Of Memes and Genes</strong></h3>
<p>Beginning about <a href="https://www.palladiummag.com/2023/11/17/genomics-has-revealed-an-age-undreamed-of/" target="_blank" rel="noopener noreferrer nofollow">twenty-five years ago</a>, geneticists finally began to look at the variation within the Indian subcontinent and were shocked by what they found. In small villages in India, Dalits, formerly called “outcastes,” were as genetically distinct from their Brahmin neighbors as Swedes were from Sicilians. In fact, a Brahmin from the far southern state of Tamil Nadu was genetically closer to a Brahmin from the northern state of Punjab than they were to their fellow non-Brahmin Tamils. Dalits from the north were similar to Dalits from the south, while the three upper castes, Brahmins, Kshatriyas, and Vaishyas, tended to cluster together against the Sudras.</p>
<p>Some scholars, like Nicholas Dirks, the former chancellor of UC Berkeley, argued for the mobility and dynamism of the caste system in their scholarship. But the genetic evidence seemed to indicate a level of social stratification that echoes through millennia. Across the subcontinent, Dalit castes engaged in menial and unsanitary labor and, therefore, were considered ritually impure. Meanwhile, Brahmins were the custodians of the Hindu Vedic tradition that ultimately bound the Indic cultures together with other Indo-European traditions, like that of the ancient Iranians or Greeks. Other castes also had their occupations: Kshatriyas were the warriors, while Vaishyas were merchants and other economically productive occupations.</p>
<p>Brahmins, Kshatriyas, and Vaishyas were traditionally the three “twice-born” castes, allowing them to study the Hindu scriptures after an initiatory ritual. The majority of the population were Sudras (or Shudras), India’s peasant and laboring majority. Shudras could not study the scriptures and might be excluded from some temples and festivals, but they were integrated into the Hindu fold and served by Brahmin priests. A traditional ethnohistory posits that elite Brahmin priests and Kshatriya rulers combined with Vaishya commoners formed the core of the early Aryan society in the subcontinent, with Shudras integrated into their tribes as indigenous subalterns. Outcastes were tribes and other assorted latecomers who were assimilated at the very bottom of the social system, performing the most degrading and impure tasks.</p>
<figure id="attachment_7069" aria-describedby="caption-attachment-7069" style="width: 2747px" class="wp-caption alignnone"><img fetchpriority="high" decoding="async" class="wp-image-7069 size-full" style="text-align: center;" src="https://pdmedia.b-cdn.net/2024/04/razib-varna-chart.png" alt="" width="2747" height="1863" srcset="https://pdmedia.b-cdn.net/2024/04/razib-varna-chart-300x203.png 300w, https://pdmedia.b-cdn.net/2024/04/u6oIGwtJ-razib-varna-chart-1024x694.png 1024w, https://pdmedia.b-cdn.net/2024/04/razib-varna-chart-768x521.png 768w, https://pdmedia.b-cdn.net/2024/04/razib-varna-chart-1536x1042.png 1536w, https://pdmedia.b-cdn.net/2024/04/razib-varna-chart-2048x1389.png 2048w, https://pdmedia.b-cdn.net/2024/04/razib-varna-chart-450x305.png 450w, https://pdmedia.b-cdn.net/2024/04/razib-varna-chart-885x600.png 885w, https://pdmedia.b-cdn.net/2024/04/razib-varna-chart.png 2747w" sizes="(max-width: 2747px) 100vw, 2747px" /><figcaption id="caption-attachment-7069" class="wp-caption-text">Razib Khan/The caste system as a layered varna system with five classes and numerous integrated jati communities.</figcaption></figure>
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<p data-pm-slice="1 1 []">This was the theory. Reality is always more complex. In India, the caste system combines two different social categories: <em>varna </em>and <em>jati</em>. <em>Varna </em>derives from the tripartite Indo-European system, represented in India by Brahmins, Kshatriyas, and Vaishyas. It literally translates as “color”: white for Brahmin purity, red for Kshatriya power, and yellow for Vaishya fertility. But India also has Shudras, black for labor. In contrast to the simplicity of <em>varna</em>, with its four classes,<em> jati </em>is fractured into thousands of localized communities. If <em>varna </em>is connected to the deep history of Indo-Aryans and is freighted with religious significance, <em>jati </em>is the concrete expression of Indian communitarianism in local places and times.</p>
<p>Though non-Indians may see in <em>varna </em>the essence of caste, in the subcontinent it is <em>jati </em>through which caste expresses itself in day-to-day life—in the U.S., <em>jati</em> is almost nonexistent for Indian Americans. Dalits, the former outcastes, may not have <em>varna </em>status, but they have numerous <em>jatis </em>across the nation. Christians, Muslims, and Buddhists who convert from Hindu Dalit <em>jatis </em>still retain their communal identity in the eyes of their new co-religionists. In the Islamic Republic of Pakistan, sanitation positions have sometimes stipulated Christian applicants only because the majority of that nation’s Christians descend from Dalit Hindu converts who engaged in those occupations.</p>
<p>The deviation of caste from <em>varna </em>theory is illustrated by the reality that in much of South India, the only twice-born caste is Brahmins; there are no Kshatriyas or Vaishyas. Rather, the kings and merchant princes of these regions hailed from Shudra <em>jatis</em>. In Gujarat and Punjab in the northwest, Brahmins may still be given religious primacy as the highest caste, but power and social status are the purview of <em>jatis</em> who engaged in trade and landowning of the Vaishya, Kshatriya, or even Shudra <em>varna</em>.</p>
<p>This incredible kaleidoscope of social complexity has played out over thousands of years across a subcontinent that spans the snowy fastness of the Himalayas in the north to the jungles of the deep tropics in the south. For decades, social scientists have speculated about the fluidity and flexibility of the caste system. But over the last generation, geneticists who have looked at the data note that various <em>jati </em>categories seem to be distinct populations which have been endogamous for thousands of years. The traditional theory, held in some suspicion, was that the three twice-born castes were originally Aryan and genetics actually confirms that these <em>jatis </em>bracketed into the Brahmin, Kshatriya, and Vaishya <em>varna </em>do indeed often have more Eurasian steppe ancestry connecting them to Europeans than regional Shudra <em>jati</em>. And Dalit castes across the subcontinent have the least steppe, ergo Aryan, ancestry.</p>
<p>The best evidence is that Indo-Aryans arrived in the Indian subcontinent between 3,500 and 4,000 years ago. This means it is likely that the <em>varna </em>system originated during this period, and the overrepresentation of steppe ancestry in the subcontinent among elites is nearly 4,000 years old! The economic historian Gregory Clark has stated that India shows the highest persistence of social status among all his data, with heritability in the range of 0.90. But there is a peculiar lacuna in the discourse around caste with its fixation on <em>varna</em>: India is the only Indo-European society with <em>jati</em>. Though, in the abstract, the ritual status of Kashmiri Pandits and Tamil Iyer Brahmins is broadly the same, these two communities speak different languages, have different attitudes to vegetarianism, and are even genetically very distinct. What matters in affinity, socialization and marriage is the <em>jati </em>of the Iyers and Pandits, not their <em>varna </em>status.</p>
<p>It is possible that <em>jati </em>was an invention of the Indo-Aryans who entered an alien landscape of incredible diversity. But there is evidence that, in fact, <em>jati </em>may predate Indo-Aryans, and it was <em>varna </em>that was overlaid atop it as a scaffold. Across South India, the non-Brahmin population ranges from regional landlords to Dalits relegated to degrading occupations. Both these groups are notionally non-Aryan, but genetically there are clear differences between Dalits and local Shudra <em>jatis</em>, indicating that Indo-Aryan culture may not be a necessary precondition for the social and genetic segregation typical of the Indian subcontinent.</p>
<h3><strong>The Past and Future of Caste</strong></h3>
<p>The Indus Valley Civilization spanned much of the northwest of the subcontinent, dominating modern Pakistan, but also extended into Indian Punjab and Gujarat. It was substantially larger than Sumer or Egypt and may, therefore, have been multiethnic. But it was also characterized by planned cities with ancient public works, like efficient sewage systems. And yet, this early Indian civilization did not seem to have thrown up palaces or exhibited much sign of inequality. The evidence from Egypt and Sumer suggests that Bronze Age cultures were hierarchical and dominated by an all-powerful ruler, but the Indus Valley Civilization defies that characterization.</p>
<p>But what if the political anarchism that seems to be suggested by the lack of centralized monumental structures at Harappa and Mohenjo-Daro, two of the largest cities of this civilization, mask the reality that these early Indians were organized around tight communal social structures that served to regulate relationships between elements of this early urban world? In other words, what if the Indus Valley Civilization was an assembly of Bronze Age <em>jatis,</em> and the <em>jatis </em>persisted as social technologies long after the cities collapsed in the wake of climatic shocks in the century before 2000 BC?</p>
<p>The tendency toward central rule in the civilizations of West and East Asia, with paramount rulers like Khufu in Egypt, <a href="https://www.palladiummag.com/2021/05/17/why-civilization-is-older-than-we-thought/" target="_blank" rel="noopener noreferrer nofollow">Sargon the Great in Akkad</a>, and <a href="https://www.palladiummag.com/2020/07/10/how-late-zhou-china-reverse-engineered-a-civilization/" target="_blank" rel="noopener noreferrer nofollow">Qin Shi Huang in China</a>, may reflect the lack of social texture and complexity in these cultures. India’s relatively decentralized character could instead reflect that many of the duties and functions of centralized states and paramount rulers fell upon the <em>jati</em>, those communities that self-organized and self-governed. To this day, caste remains a feature of the Indian republic’s constitution, prohibiting discrimination but also carving out set-asides for Dalits and lower castes. The Indian state, modeled on British norms, must still grapple with the reality of caste, and many Indian political parties have been implicitly and explicitly reflections of castes.</p>
<p>Indian caste, unlike the Chinese mandarin system and even the European blood nobility, was predicated on an extreme level of fine-grained endogamy. Across much of India, the rate of out-marriage seems to be 0.5% per generation within local villages, divided between a handful of customary communities and often dominated by one <em>jati</em>. The social and cultural forces necessary to induce this level of adherence to norms and values are difficult for Westerners to imagine, but Indian villages may be thought of as early-modern total states where everyone was in everyone else’s business.</p>
<p>But the current endogamy rates in the subcontinent, closer to 90% than 99%, mean that this thousand-year institution is not going to persist for more than a few more centuries. Without the ties of endogamy inducing social cohesion, India will develop a more conventional class system defined by more fluidity and flexibility. But what will happen when humanity leaves the gravity well of the Earth?</p>
<p>Will future Martians intermarry with future Terrans? Will colonies in the asteroid belt promiscuously interact with each other? The <a href="https://www.nbcnews.com/storyline/the-big-questions/mars-colonists-might-evolve-entirely-new-type-human-n708636" target="_blank" rel="noopener noreferrer nofollow">conventional understanding</a> of the human spacefaring future is that we face the threat of speciation. But speciation implies total isolation and separation. Perhaps we might better think of the human future as a constellation of endogamous subpopulations united by communication systems and a common ethos into which they inflected their own communal norms. Perhaps the distant human future will again be of different castes, each specially oriented toward their ideal occupations and living in close quarters in artificial habitats. India’s long history shows that humans are capable of such a complex yet stable equilibrium.</p>
<div class="author-bio">
<p class="author-description">Razib Khan is a co-founder <a href="https://www.genrait.com/">GenRAIT</a>, a deep tech company that deploys a platform for the life sciences. He also writes at Razib Khan’s <a href="https://www.razibkhan.com/">Unsupervised Learning</a>. You can follow him at <a href="https://twitter.com/razibkhan">@razibkhan</a>.</p>
</div>The post <a href="https://www.palladiummag.com/2024/04/05/as-caste-vanishes-only-genes-remain/">As Caste Vanishes Only Genes Remain
</a> appeared first on <a href="https://www.palladiummag.com/">Palladium</a>.]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">7063</post-id>	</item>
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		<title>The Native Americans Before the Native Americans
</title>
		<link>https://www.palladiummag.com/2024/02/02/the-native-americans-before-the-native-americans/</link>
		
		<dc:creator><![CDATA[Razib Khan]]></dc:creator>
		<pubDate>Fri, 02 Feb 2024 17:11:20 +0000</pubDate>
				<category><![CDATA[Articles]]></category>
		<guid isPermaLink="false">https://www.palladiummag.com/?p=6997</guid>

					<description><![CDATA[<p>New findings and genetic evidence suggest that people came to America more than 30,000 years ago, before the peak of the last ice age.</p>
The post <a href="https://www.palladiummag.com/2024/02/02/the-native-americans-before-the-native-americans/">The Native Americans Before the Native Americans
</a> appeared first on <a href="https://www.palladiummag.com/">Palladium</a>.]]></description>
										<content:encoded><![CDATA[<p><span style="font-weight: 400;">In 2021, scientists radiocarbon-dated pollen found in human footprints at the White Sands National Park in New Mexico and came back with dates of greater than 20,000 years. Critics demanded more evidence, and in 2023, </span><a href="https://www.nature.com/articles/s41586-020-2491-6"><span style="font-weight: 400;">using new data and more advanced methods</span></a><span style="font-weight: 400;"> seems to have confirmed the date. Though there are still skeptics, the White Sands discovery is not the only site that dates to the Last Glacial Maximum between 20-26,000 years ago.</span></p>
<p><span style="font-weight: 400;">For decades, paleoanthropologists believed the ancestors of American natives were a Siberian tribe that came over from Asia to North America just 13,500 years ago, crossing over Beringia, a landmass exposed by sharply reduced sea levels during the last Ice Age. They called these people the Clovis Culture based on distinct spear points first discovered next to the remains of mammoths at a site in New Mexico. The paradigm posited that over 300 years these big game hunters spread across the New World, driving megafauna into extinction and eventually diversifying into the people we know today as Native Americans. </span></p>
<p><span style="font-weight: 400;">Yet, already 25 years ago, the evidence contradicting this paradigm became quite strong. There were too many sites that predated Clovis by centuries. Monte Verde in Chile, where archaeologists have been excavating since 1977, is extensively documented and is </span><a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141923"><span style="font-weight: 400;">over 1000 years older</span></a><span style="font-weight: 400;"> than Clovis. In Mexico, Chiquihuite Cave has yielded 1900 stone artifacts, and dates were returned as early as 31-33,000 years ago, long before the Last Glacial Maximum. Being more conservative, the researchers at this site are convinced that humans were claiming it 20,000 years ago at the latest. These dates imply that this population, presumably part of the same group that was leaving footprints at White Sands National Park, arrived much earlier because the expansion of the ice sheets beginning 26,000 years ago definitively blocked the interior migration path and would have made a sea-borne route along the western periphery very difficult as glaciers pushed to the edge of the Pacific.</span></p>
<p><span style="font-weight: 400;">In 2014, </span><a href="https://www.bbc.com/news/science-environment-25020958"><span style="font-weight: 400;">geneticists discovered and sequenced</span></a><span style="font-weight: 400;"> the 24,000-year-old remains of a boy who died on the shores of Lake Baikal and concluded that people related to him contributed 10-15% of the ancestry of modern Europeans and 40% of the ancestry of Native Americans. In one fell swoop, earlier anthropological and genetic suspicions of connections between the two populations were explained. Then, </span><a href="https://www.smithsonianmag.com/science-nature/dna-search-first-americans-links-amazon-indigenous-australians-180955976/" class="broken_link"><span style="font-weight: 400;">in 2015</span></a><span style="font-weight: 400;">, the same group of geneticists found that some tribes in the Amazon had ancestry which tied them more closely to Australian Aboriginals and Papuans than to Siberians! This seemed to be a crazy result, but follow-up work not only confirms its correctness, but shows that this exotic ancestry is found across the </span><a href="https://www.pnas.org/doi/10.1073/pnas.2025739118" class="broken_link"><span style="font-weight: 400;">central band of South America</span></a><span style="font-weight: 400;">, from the coast into the Amazon.</span></p>
<p><span style="font-weight: 400;">The latest </span><a href="https://www.nature.com/articles/s41586-020-2491-6"><span style="font-weight: 400;">controversial but methodologically cutting-edge models</span></a><span style="font-weight: 400;"> imply that humans arrived in the New World more than 30,000 years ago, long before the proto-Beringian population was even hypothesized to exist. The world we thought we knew in the 1990s turns out not to be anything close to the world that might have been. Over the last 25 years, there has been a revolution in our understanding of how the first humans arrived in the Americas and who they were. But these revelations have not illuminated the totality of the past; there still are dragons in the blank spots in our map of this surprisingly ancient New World. </span></p>
<h3><b>Native Americans And Europeans Share Paleo-Siberian Ancestors</b></h3>
<p><span style="font-weight: 400;">Some of the more sensational arguments on the ancestry of Native Americans turn out to have fallen flat. The Solutrean hypothesis, which argued that Native Americans descended at least in part from an Ice Age European culture that flourished 20,000 years ago based on similarities between that culture’s tools and that of the Clovis people, is clearly wrong. The similarities in tool types, separated by 4000 years between the extinction of the former and the emergence of the latter, are likely just convergence, the product of the constraints in functionality and physics.</span></p>
<figure id="attachment_6994" aria-describedby="caption-attachment-6994" style="width: 730px" class="wp-caption aligncenter"><img decoding="async" class="wp-image-6994 size-full" src="https://pdmedia.b-cdn.net/2024/02/76d47daa-86cc-4c32-b173-635fe67d90cc_730x487.jpg" alt="" width="730" height="487" srcset="https://pdmedia.b-cdn.net/2024/02/76d47daa-86cc-4c32-b173-635fe67d90cc_730x487-300x200.jpg 300w, https://pdmedia.b-cdn.net/2024/02/xK0CXip0-76d47daa-86cc-4c32-b173-635fe67d90cc_730x487-450x300.jpg 450w, https://pdmedia.b-cdn.net/2024/02/76d47daa-86cc-4c32-b173-635fe67d90cc_730x487.jpg 730w" sizes="(max-width: 730px) 100vw, 730px" /><figcaption id="caption-attachment-6994" class="wp-caption-text">Bill Whittaker/North American spearpoints that appear to be precursors to later Clovis points</figcaption></figure>
<p><span style="font-weight: 400;">You don’t need fancy genetics to reach this conclusion. Not only do many native peoples of the New World look like they have anthropological affinities with the people of eastern Eurasia, but 20th-century physical anthropological metrics like the shape of teeth or the dimensions of the skull tended to cluster Native Americans with East Asians. Additionally, before the Norse, all the evidence points to contacts with Asia rather than the continent to North America’s east. The native peoples of the Arctic clearly have cultural connections to the indigenous tribes of far east Siberia, in particular the Chukchi. </span></p>
<p><span style="font-weight: 400;">This contact was profoundly impactful in the first millennium AD when the recurved Asian war bow </span><a href="https://onlinelibrary.wiley.com/doi/10.1002/evan.21357" class="broken_link"><span style="font-weight: 400;">arrived</span></a><span style="font-weight: 400;"> in Alaska in the 7th century AD over the Bering Strait, to be followed several centuries later by laminar armor familiar from medieval Japan. The New World is characterized by stark isolation, with North American civilizations at the late Neolithic and early Bronze Age stages of complexity when Eurasia was on the precipice of early modernity, but it was also permeable across the sieve of the circumpolar world.</span></p>
<p><span style="font-weight: 400;">A physical anthropologist once told me that even after more than 10,000 years, the indigenous people of the Amazon retain “Siberian proportions”—shorter legs and arms and a longer torso. In many ways, it is easier for cold-adapted people to flourish in the tropics; after all, our lineage was originally tropical, and the cultural toolkit for the cooler latitudes can simply be discarded—literally, in the case of clothes. The world of the early Amerindians was not the lush and verdant Amazon basin; it was the vast expanse of land exposed during the last Ice Age between Alaska and Siberia, Beringia. Here they arrived 20,000 years ago, likely following herds of mammoth on its north slope, on the tundra facing the Arctic, while they exploited marine resources in the south, along the seas characterized by fog and peat-bogs. </span></p>
<p><span style="font-weight: 400;">Genetic and anthropological work with blood groups and skeletal features established that the closest population to New World natives were the people of East Asia, supporting the theory promoted by geologist David Hopkins in the 1960s of a migration over a Bering land bridge. Nevertheless, simple physical inspection yielded the inference that these were not quite the same people as those of China, Korea, and Japan. Geography pointed to Siberia, but even here, the modern-day Yakut looks somewhat different from Native Americans, who often have prominent aquiline noses. Of course, aquiline noses are common in western Eurasia, suggesting possible connections with Europeans.</span></p>
<p><span style="font-weight: 400;">The answer was prefigured by paternal lineage as traced through the genealogy transmitted from father to son. By the first decade of the 21st century, it was clear that the overwhelming majority of Native American Y chromosome lineages belong to the Q haplogroup—the class of related men bracketed together as a distinct cluster with a common ancestor defined by informative mutations. </span></p>
<p><span style="font-weight: 400;">The nomenclature of Y chromosomes is alphabetic, and the closest “sibling” to Q is R, which, in the forms of R1a and R1b, is the dominant haplogroup in Europe. The Y chromosomal data points to a genetic relationship between the forefathers of Europeans and Native Americans, which remained inexplicable. More suggestively, in 2012, a new method of constructing genetic relationships that use graphs or networks instead of trees, with the gene flow represented by “edges” connecting different branches, yielded a hypothetical migration on the schematic </span><a href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002967"><span style="font-weight: 400;">connecting</span></a><span style="font-weight: 400;"> Europeans and Native Americans. Though this jumped out of the data, there was no historical paradigm to integrate the result. </span></p>
<p><span style="font-weight: 400;">Two years later, the Ma’lta boy, dating to 24,000 years ago, was the first of many finds from Siberia where ancient DNA provided the “missing link” between these two populations, one in the New World and the other at the western antipode of Eurasia. The perplexities of the past could finally find an elegant explanation. </span><span style="font-weight: 400;"><br />
</span><span style="font-weight: 400;"><br />
</span><span style="font-weight: 400;">After the expansion of modern humans into Eurasia more than 45,000 years ago, one branch of </span><i><span style="font-weight: 400;">Homo sapiens</span></i><span style="font-weight: 400;"> related to the foragers of Pleistocene Europe continued to move eastward until their furthest outliers reached northeastern Siberia. Called “Ancient North Eurasians” (ANE) by scholars, no human population is a direct singular descendent of this group. Modern Siberians descend predominantly from later waves of migrants from East Asia, </span><a href="https://www.palladiummag.com/2023/11/17/genomics-has-revealed-an-age-undreamed-of/"><span style="font-weight: 400;">who absorbed</span></a><span style="font-weight: 400;"> the first modern human populations.</span></p>
<figure id="attachment_6993" aria-describedby="caption-attachment-6993" style="width: 2560px" class="wp-caption aligncenter"><img decoding="async" class="wp-image-6993 size-full" src="https://pdmedia.b-cdn.net/2024/02/73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095.jpg" alt="" width="2560" height="1095" srcset="https://pdmedia.b-cdn.net/2024/02/73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095-300x128.jpg 300w, https://pdmedia.b-cdn.net/2024/02/hyl7ZQOq-73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095-1024x438.jpg 1024w, https://pdmedia.b-cdn.net/2024/02/73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095-768x329.jpg 768w, https://pdmedia.b-cdn.net/2024/02/73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095-1536x657.jpg 1536w, https://pdmedia.b-cdn.net/2024/02/73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095-2048x876.jpg 2048w, https://pdmedia.b-cdn.net/2024/02/hyl7ZQOq-73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095-450x192.jpg 450w, https://pdmedia.b-cdn.net/2024/02/73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095-1360x582.jpg 1360w, https://pdmedia.b-cdn.net/2024/02/73428372-b173-42ce-b0de-7e66fae0fb4f_2560x1095.jpg 2560w" sizes="(max-width: 2560px) 100vw, 2560px" /><figcaption id="caption-attachment-6993" class="wp-caption-text">NaturalEarthData.com/Map of Ancient North Eurasian (ANE) dispersion.</figcaption></figure>
<p><span style="font-size: 1em; letter-spacing: 0px; text-align: center;">The ancestors of Native Americans are often called, originally, “Paleo-Siberians,” a fusion of ANE and East Asians moving up from the south. Though the overall ancestry, around 65%, tilts toward East Asians, the paternal lineage is biased toward the remainder, the ANE heritage. The ANE and East Asian ancestors of Native Americans seem to have diverged from the ancestors of the populations that later contributed to modern Siberians and Europeans between 20-25,000 years ago.</span></p>
<h3><b>Walking From Siberia to Alaska, Sailing to America</b></h3>
<p><span style="font-weight: 400;">As sea levels dropped 400 feet lower than today during the Last Glacial Maximum, a vast tundra opened up between the eastern tip of Siberia and northern Alaska. This now sunken land was a prime megafauna habitat. Despite its northern location, this dry ecosystem was not glaciated and likely supported large human populations that followed the migration of mammoths. In contrast, the area to the south—the exposed land that is today the northern Bering Strait—was dominated by peat bogs, and any forager populations would likely have had to rely on marine resources. Rather than a single tribe with a single culture, the early Beringians were likely adapted to numerous local ecologies.</span></p>
<p><span style="font-weight: 400;">And yet, these people did not move east and into North America; the Last Glacial Maximum resulted in the expansion of the Cordilleran and Laurentide ice sheets in western and eastern North America, closing a potential path through the interior of North America. The ice age closed as many paths as it opened. The best data indicates that these two ice sheets did not open a corridor until 14,000 years ago, post-dating evidence of human occupation in Monte Verde in Chile by 500 years.</span></p>
<figure id="attachment_6992" aria-describedby="caption-attachment-6992" style="width: 2048px" class="wp-caption aligncenter"><img loading="lazy" decoding="async" class="size-full wp-image-6992" src="https://pdmedia.b-cdn.net/2024/02/700d3521-26ac-40e4-91a4-fb4c7d9c95fb_2048x1389.png" alt="" width="2048" height="1389" srcset="https://pdmedia.b-cdn.net/2024/02/700d3521-26ac-40e4-91a4-fb4c7d9c95fb_2048x1389-300x203.png 300w, https://pdmedia.b-cdn.net/2024/02/7ZIFOyQV-700d3521-26ac-40e4-91a4-fb4c7d9c95fb_2048x1389-1024x695.png 1024w, https://pdmedia.b-cdn.net/2024/02/700d3521-26ac-40e4-91a4-fb4c7d9c95fb_2048x1389-768x521.png 768w, https://pdmedia.b-cdn.net/2024/02/700d3521-26ac-40e4-91a4-fb4c7d9c95fb_2048x1389-1536x1042.png 1536w, https://pdmedia.b-cdn.net/2024/02/700d3521-26ac-40e4-91a4-fb4c7d9c95fb_2048x1389-450x305.png 450w, https://pdmedia.b-cdn.net/2024/02/700d3521-26ac-40e4-91a4-fb4c7d9c95fb_2048x1389-885x600.png 885w, https://pdmedia.b-cdn.net/2024/02/700d3521-26ac-40e4-91a4-fb4c7d9c95fb_2048x1389.png 2048w" sizes="auto, (max-width: 2048px) 100vw, 2048px" /><figcaption id="caption-attachment-6992" class="wp-caption-text">U.S. National Park Service/Map of the ancient Beringia region.</figcaption></figure>
<p><span style="font-weight: 400;">Rather than indefatigable mammoth hunters killing their way through the interior, the Beringians likely arrived in the New World along the western fringe of North America, hugging the coast and hopping across islands as marine foragers. Island hopping was feasible beginning 17,000 years ago, resulting in pockets of human occupation along the southern Alaskan coast while the sea levels began to rise as the Ice Age abated.</span></p>
<p><span style="font-weight: 400;">While genetic evidence strongly points to a bottleneck that began around 20,000 years ago, the archaeological evidence strongly points to the opening of a viable path southward into the Americas after 17,000 years ago. This 3000 years or so is sometimes termed the “Beringian standstill,” when the ancestors of the Native Americans occupied ecologically favored territory east of Siberia but were blocked by ice sheets from moving further east into North America. </span></p>
<p><span style="font-weight: 400;">Over these more than one hundred generations, a homogeneous genetic population emerged in Beringia, isolated from populations to the east. The genetic influences evidenced in eastern Siberians and the Inuit, who arrived to the Arctic long after the Ice Age, are not present in Native Americans because their Beringian ancestors were sealed off from Eurasia, first by the extreme conditions of the Last Glacial Maximum and then rising sea levels, which broke the connection between the Americas and Eurasia. </span></p>
<p><span style="font-weight: 400;">Looking at the genetic network of haplogroup Q, more than 90% of full-blooded Native American males, a massive demographic expansion seems to have occurred around 14,000 years ago, just before the rise of the Clovis people, along with a later expansion in South America 12,000 years ago. This, seemingly, was most of the story. </span></p>
<p><span style="font-weight: 400;">The Na-Dene people of western North America, most prominent of whom are the Navajo tribe, have more East Asian ancestry, and observers have long-observed their more East Asian features, while the Paleo-Eskimos and the Thule Culture of the modern Inuit date to the period after 3000 BC. Though the source and timing of the Na-Dene migration has not been entirely established, ancient DNA makes it seem likely that they arrived after the end of the Ice Age, but before the Paleo-Eskimos. </span></p>
<p><span style="font-weight: 400;">A fusion between two Siberian groups more than 20,000 years ago gave Native Americans ties to populations of western and southern Eurasia. A later migration eastward was halted by glaciers, until a final radiation began to occur 15,000 years ago, likely through the Pacific route, and then a switch to big game mammoth-hunting again with the Clovis people. Finally, secondary supplementary migrations from Siberia during the Holocene point to the long-term periodic exchanges across the Bering Strait that continued after the sea levels rose. But this was not to be the end of what genetics told us. </span></p>
<h3><b>Cousins on Opposite Ends of the Pacific Ocean</b></h3>
<p><span style="font-weight: 400;">For many decades, geneticists had access to the samples from two tribes in the Amazon, the Karitiana and the Surui. Earlier methodologies showed they were similar to other native peoples of the New World, except they were more isolated and genetically homogeneous, indicating a bottleneck due to small population sizes. But by the middle of the 2010s, geneticists were applying more robust and rigorous methods to pry out any aberrations or novelties in the broadly-sketched earlier genetic relationships. </span></p>
<p><span style="font-weight: 400;">Looking at hundreds of thousands of genetic markers across hundreds of individuals, the researchers noticed a subtle but clear signal of affinity between the Amazonian trib</span><span style="font-weight: 400;">es and their Australasian samples, which included Onge from the Andaman Islands in the Bay of Bengal, Papuans, and indigenous Australians. The results were so surprising that the researchers repeated the analysis over and over, and in the last decade, others have also found the same result, even more broadly in modern South America. Calling it “Population Y,” the signature appeared in only one ancient individual from Brazil dated to 8400 BC and is lacking in all other early Amerindian samples. To this day, this genetic signature is mysterious in terms of its provenance and what it tells us about the peopling of the New World. There are three major explanations for how this signal came to be present across contemporary South America.</span></p>
<p><span style="font-weight: 400;">One hypothesis, crazy as it might seem, is that a group of Melanesians crossed the Pacific and mixed with the descendants of Beringians. Since the oldest Brazilian individual who carries this signature lived only 1000 years after the Ice Age, this would open up the strange possibility of Pleistocene mariners. Another less strange possibility is the Beringians had an internal population structure. This is just a fancy way of saying that, in fact, the early Beringians were not homogeneous and well-admixed, but some tribes had different ancestry from others. When there was a massive push southward between 15,000 and 16,000 years ago, some populations that moved into South America carried Population Y ancestry, and they persisted as an independent structured population down to the present. </span></p>
<p><span style="font-weight: 400;">At this point you might be wondering how Melanesians got to Siberia, but the reality here is that it may not be that Population Y is Melanesian at all, just that that’s the closest modern population in the databases. When you look at the genetics of the people of the world east beyond India, there is a clear divide between the north and the south that seems to date back to more than 40,000 years ago. The southern populations include Melanesians, Australians, Andaman Islanders, and the Negritos of Malaysia and the Philippines. The northern populations include Siberians, Han Chinese, and Japanese, as well as most Southeast Asians. However, the current distribution of these populations was </span><a href="https://www.palladiummag.com/2023/11/17/genomics-has-revealed-an-age-undreamed-of/"><span style="font-weight: 400;">not always the same</span></a><span style="font-weight: 400;">. </span></p>
<p><span style="font-weight: 400;">At the end of the last Ice Age, the southern branch was dominant as far north as China, with Neolithic Age farmer migrations southward slowly erasing its signal until there were only relict populations remaining. And, interestingly, it seems that Ice Age Tibetans were also more genetically related to the southern population than the northern one. This is still clear in the Y chromosomal haplogroup they share with Andamanese, D, as well as many Japanese, indicating more complexity in ancient East Asia than we are used to imagining. It is entirely possible that during the Ice Age, some “southern” populations were present in Siberia, considering that Tibet was a reservoir of one of these peoples.</span></p>
<h3><b>A People in America Before the Beringians</b></h3>
<p><span style="font-weight: 400;">Though there is nothing impossible about the persistence of ancient structure in Beringia for thousands of years—after all, the Hindu caste system has maintained genetic structure for at least 1500 years—it is less parsimonious than one more explanation for population Y—that it was an earlier group than Beringians that was later absorbed in South America. </span></p>
<p><span style="font-weight: 400;">This would explain why the signal is not present in any ancient samples from Alaska or North America; population Y simply did not leave an imprint on the northerners. It would obviate the need to maintain genetic substructure in Beringia, as population Y was presumably south and east of the glaciers when the Beringians were coalescing on the Arctic tundra. Population Y being an earlier arrival to the New World before the Beringians is attractive as a hypothesis as it explains the now substantial archeological evidence that there were earlier Americans before the Last Glacial Maximum.</span></p>
<p><span style="font-weight: 400;">A speculative model then beckons that an early branch of humanity distantly related to Melanesians crossed from Asia to North America just as Ancient North Eurasians were pushing east into Siberia. In all likelihood, these people were coastal foragers and may have had some primitive vessels. If they arrived before the Last Glacial Maximum, they would have had the New World for tens of thousands of years to themselves. But this presents a conundrum: where are their human remains? </span></p>
<p><span style="font-weight: 400;">Archaeologists have been able to find primitive tools that date to this early period, though there are still disputes about dating and the human-created nature of the stone flakes. No ancient DNA or fossil has been found at these Last Glacial Maximum and earlier sites. But to be fair, much the same could be said for the pre-Clovis Beringians, who are now understood to have existed. With the exception of coprolites from </span><a href="https://www.science.org/doi/10.1126/sciadv.aba6404" class="broken_link"><span style="font-weight: 400;">Paisley Caves</span></a><span style="font-weight: 400;"> in Oregon, they too left no human remains. More curiously, the massive explosion of sites, human remains, and megafaunal extinctions that date to the Clovis period, starting 13,500 years ago, suggests a huge ramp-up of the anthropogenic impact of our species qualitatively different from what came before.</span></p>
<p><span style="font-weight: 400;">The genetic and archaeological data now point to the tentative but plausible possibility that humans were present before the Last Glacial Maximum, though very sparse on the ground and highly mobile. These people were likely very distantly related to the people of Australasia rather than the main line of East Asians or the western-related ANE. The presence of Y chromosomal haplogroup D among the Japanese, derived from the indigenous Jomon who were resident in the islands for more than 10,000 years, shared with Andamanese and Tibetans, presents a scenario where beach-combing foragers drift upward from Southeast Asia and eventually across the north Pacific littoral. </span></p>
<p><span style="font-weight: 400;">In the thousands of years they occupied the New World, their impact on the local ecosystems was marginal; there was no massive megafaunal die-off as occurred in Australia or the New World after the Last Glacial Maximum. The absence of human remains indicates a very low-density mobile population, perhaps tied predominantly to the sunken shorelines of the Pleistocene. Today, environmentalists idealize the native people of the New World, but as Charles C. Mann has written in </span><i><span style="font-weight: 400;">1492 </span></i><span style="font-weight: 400;">and</span><i><span style="font-weight: 400;"> 1493</span></i><span style="font-weight: 400;">, the Amerindians were much more complicated than that, resculpting the landscape with fire and driving charismatic creatures like mammoths to extinction. </span></p>
<p><span style="font-weight: 400;">Early reports of scientists discovering large settlements in the Amazon have now been confirmed with </span><a href="https://www.bbc.com/news/science-environment-67940671"><span style="font-weight: 400;">21st-century surveying technology</span></a><span style="font-weight: 400;">. The greatest rainforest in the world might have been subject to extensive terraforming, and tribes like the Kariatania and Surui aren’t so much untouched hunter-gatherers but the descendants of fallen civilizations wandering a post-apocalyptic world.</span></p>
<p><span style="font-weight: 400;">There may also have been those who came before, leaving telltale marks in the genomes of modern Amazonians and their neighbors to the west along the Pacific coast. Their genetics and date of arrival indicate they were modern humans, but like Neanderthals and Denisovans, they did not reshape the ecology and biodiversity of their locales with a blitzkrieg of human exploitation or demographic excess. In this way, the Beringians resembled the Europeans that would conquer them thousands of years later, rather than the earliest of all Americans.</span></p>
<h3><b>The Enduring Mystery of the New World</b><b></b></h3>
<p><span style="font-weight: 400;">Perhaps the New World, in the end, is the greatest anthropological experiment of all, recording a society of modern</span><i><span style="font-weight: 400;"> Homo sapiens</span></i><span style="font-weight: 400;"> that doesn’t drive megafauna to extinction—Mother Nature’s mostly independent and newer trial run of the human species, distinct from the earlier and separate creation of the Old World of Afro-Eurasia and Near Oceania. Far Oceania is, however, known to have </span><a href="https://www.nature.com/articles/s41586-020-2487-2"><span style="font-weight: 400;">experienced</span></a><span style="font-weight: 400;"> a genetic imprint of Amerindians, perhaps through captives brought back from the South American mainland and the transmission of the South American sweet potato to the Pacific peoples. </span></p>
<p><span style="font-weight: 400;">When Hernán Cortés arrived in Mexico, the pre-metal age civilization of the Aztecs was reminiscent of 1492 BC rather than 1492 AD to the Spaniards. Not only were the Aztecs heathens, but they were still sacrificing humans in blood rituals, a practice stamped out in Europe by the pagan Romans in their conquest of the Celts 2000 years ago. Upon realizing they had not stumbled upon the Indies, Europeans began calling it </span><i><span style="font-weight: 400;">Mundus Novus</span></i><span style="font-weight: 400;">, or the New World. Though pre-modern geography and anthropology were filled with blank spaces on the map, by 1492, the centuries-earlier </span><i><span style="font-weight: 400;">Pax Mongolica </span></i><span style="font-weight: 400;">had removed the veil of mystery from China for most Westerners. Leading up to the arrival of Europeans in Hispaniola, the Portuguese were pushing their way inexorably around Africa, tracing the outline of what was to remain the Dark Continent until the 1800s.</span></p>
<figure id="attachment_6998" aria-describedby="caption-attachment-6998" style="width: 2560px" class="wp-caption aligncenter"><img loading="lazy" decoding="async" class="wp-image-6998 size-full" src="https://pdmedia.b-cdn.net/2024/02/palladium-native-americans-4-scaled.jpg" alt="" width="2560" height="2161" srcset="https://pdmedia.b-cdn.net/2024/02/palladium-native-americans-4-300x253.jpg 300w, https://pdmedia.b-cdn.net/2024/02/riNtXGVW-palladium-native-americans-4-1024x864.jpg 1024w, https://pdmedia.b-cdn.net/2024/02/palladium-native-americans-4-768x648.jpg 768w, https://pdmedia.b-cdn.net/2024/02/palladium-native-americans-4-1536x1296.jpg 1536w, https://pdmedia.b-cdn.net/2024/02/palladium-native-americans-4-2048x1729.jpg 2048w, https://pdmedia.b-cdn.net/2024/02/palladium-native-americans-4-450x380.jpg 450w, https://pdmedia.b-cdn.net/2024/02/palladium-native-americans-4-711x600.jpg 711w, https://pdmedia.b-cdn.net/2024/02/palladium-native-americans-4-scaled.jpg 2560w" sizes="auto, (max-width: 2560px) 100vw, 2560px" /><figcaption id="caption-attachment-6998" class="wp-caption-text">Daderot/Archaic Indian copper artifacts, 3000 BC-1000 BC, exhibited in the Wisconsin Historical Museum, Madison, Wisconsin, USA.</figcaption></figure>
<p><span style="font-weight: 400;">But with Christopher Columbus’ navigation across the Atlantic, entire continents of races and civilizations were discovered, with immediate cultural consequences like Thomas More setting his </span><i><span style="font-weight: 400;">Utopia</span></i><span style="font-weight: 400;"> in the New World and Shakespeare’s play </span><i><span style="font-weight: 400;">The Tempest </span></i><span style="font-weight: 400;">clearly influenced by English contact with North America. The Western understanding of what they had discovered, or perhaps more accurately made contact with, unfolded over centuries. When it comes to Western understanding of the ancient history of this New World, it unfolds still. </span></p>
<p><span style="font-weight: 400;">The world that the Greeks and Romans had known was not the entire world; there were deep mysteries in the universe hidden even from the ancients. Early Americans in the decades after U.S. independence still hadn’t come to terms with the native peoples of the continent, whether it be their political and social role in the young republic as citizens or not or their origins as a race. The religion founded by Joseph Smith, Mormonism, was bathed with cutting-edge scientific and historical theories from the 1820s, like that Native Americans descended from ancient Hebrew tribes. Today, we might laugh at Mormons. Yet do we really know the truth either? There are mysteries in the world still, even in 2024.</span></p>
<p><span style="font-weight: 400;">Perhaps in some strange way, More’s </span><i><span style="font-weight: 400;">Utopia </span></i><span style="font-weight: 400;">captured the possibilities of the New World, though in a way he would never have anticipated. And yet the archaeological and genetic record is also clear that if these earlier people existed, they are but shadows, overwhelmed and absorbed by the Beringians, forged into the bitter coldness of the Arctic 20,000 years ago. Though the Beringians clung to the cold edge of the New World for thousands of years, it seems clear that, 13,500 years ago, the material and social technology of the Clovis Culture unlocked their human rapacity, with the extinction of mammoths, sloths, and all their predators, followed by the demographic radiation all across South America replacing any earlier arrivals. The New World became just as </span><a href="https://www.palladiummag.com/2023/11/17/genomics-has-revealed-an-age-undreamed-of/"><span style="font-weight: 400;">the Old</span></a><span style="font-weight: 400;"> was to be, both worlds born in blood and conquest.</span></p>
<div class="author-bio">
<p class="author-description">Razib Khan is a co-founder <a href="https://www.genrait.com/">GenRAIT</a>, a deep tech company that deploys a platform for the life sciences. He also writes at Razib Khan’s <a href="https://www.razibkhan.com/">Unsupervised Learning</a>. You can follow him at <a href="https://twitter.com/razibkhan">@razibkhan</a>.</p>
</div>The post <a href="https://www.palladiummag.com/2024/02/02/the-native-americans-before-the-native-americans/">The Native Americans Before the Native Americans
</a> appeared first on <a href="https://www.palladiummag.com/">Palladium</a>.]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">6997</post-id>	</item>
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		<title>Genomics Has Revealed An Age Undreamed Of
</title>
		<link>https://www.palladiummag.com/2023/11/17/genomics-has-revealed-an-age-undreamed-of/</link>
		
		<dc:creator><![CDATA[Razib Khan]]></dc:creator>
		<pubDate>Fri, 17 Nov 2023 14:08:58 +0000</pubDate>
				<category><![CDATA[Articles]]></category>
		<guid isPermaLink="false">https://www.palladiummag.com/?p=6784</guid>

					<description><![CDATA[<p>The genomics revolution has shown us our barbaric past. It now also forces us to decide our future.</p>
The post <a href="https://www.palladiummag.com/2023/11/17/genomics-has-revealed-an-age-undreamed-of/">Genomics Has Revealed An Age Undreamed Of
</a> appeared first on <a href="https://www.palladiummag.com/">Palladium</a>.]]></description>
										<content:encoded><![CDATA[<p>On June 26, 2000, President Bill Clinton announced the completion of the draft of the human genome at a press conference with the two project leads, Francis Collins and J. Craig Venter. A genome is all the genetic information of an organism. Scientists had conceived of the Human Genome Project in the 1980s, and, in the first half of the 1990s, expected it to be an endeavor that would go on for decades. But an unexpected technological revolution of faster computers and better chemistry accelerated the ten-year effort toward the finish line, just as the 20th century came to a close.</p>
<p>The American-led international effort cost more than $3 billion dollars and involved thousands of people. Since then, the last 23 years of the 21st century have seen a sea change in the landscape of genomics, from blue-sky basic science to mass-market consumer products. Companies like Nebula now provide entire genome sequences that are medical-grade quality for $200; down from a price point of $20,000 just 13 years ago. We’ve gone from a single mapped genome—that of humanity—to more than a million genomes. This is a case where quantity has a quality all its own; the commoditization of genomic sequencing has radically transformed how we do genetics.</p>
<p>Yet at the dawn of this brave new genomic era, it is not health and well-being outcomes that have been revolutionized. Rather, genomics as a window into the human past has vindicated Alfred Tennyson’s poetic assertion that nature is “red in tooth and claw.” Where a few decades ago archaeologists and historians had to cobble together inferences from pottery shards, slotting their data into theories that owed more to political fashions of the present than scientific facts of the past, today they can chart the rise and fall of peoples from the clear evidence of the genes.</p>
<p>Collins and Venter promised a shiny future of good health and a more enlightened understanding of humanity’s place in the world, but their invention has, instead, unleashed knowledge of a bygone age of brutality reminiscent of Conan the Barbarian’s Hyperborean Age. Historians can list Genghis Khan’s concubines, but it is genetics that tells us that 10% of Central Asian men are his direct paternal descendants, bringing home the magnitude of his conquests. But obviously, we aren’t fated to relive the brutality of the past; just as technology can open a window back in time, it can unlock the door to a brighter future. The question is what advances we as species wish to make.</p>
<h3>The Book of Nature Has a Billion Pages</h3>
<div>
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<p>A single human genome has two copies of each gene, of which there are 19,000. These 19,000 genes are distributed across three billion base pairs of adenine, cytosine, guanine, and thymine, or ACGT for short. Notably, the number of genes that humans have has been discovered only within the last twenty years, even though genetics as a scientific field is over 150 years old. The reason for this recent explosion in our knowledge is that, before the 1990s, genetics probed a digital process—the recombination of discrete units of heredity from the same and different individuals—with analog means. The correlation of characteristics between parents and offspring is intuitively obvious, but the mechanisms by which inheritance occurs are not self-evident.</p>
<p>Our naïve assumption is that the characteristics blend together, resulting in a child who is a synthesis of the traits of the parents e.g. a short parent and a tall parent will produce medium-height offspring. But the implication of this model is that, over the generations, all human variation should be blended away as each generation is the average of the previous one. That simply does not occur. Humans remain as variable as they have been in the past. The insight of Mendelian genetics is that inheritance does not proceed through blending, but through the rearrangement of discrete units of variation.</p>
<p>At about the same time that Charles Darwin was revolutionizing our understanding of the tree of life with his theory of evolutionary change through natural selection, an Austrian monk named Gregor Mendel stumbled upon the framework that would later be called genetics. Between 1856 and 1863, he realized that inheritance seemed to be mediated by particular units of inheritance he called “factors,” and would later be called genes. Mendel hypothesized complex organisms had two copies of many factors, discrete bundles of information that were rearranged every generation through the law of segregation—that you inherit one copy of a gene from each parent—and the law of independent assortment, that you inherit factors independently from each other.</p>
<p>Mendel came to these insights through a famous set of experiments where he crossed lines of peas with distinct characteristics and noted that some traits bred true and others did not. Two short pea plants always produced short pea plants. But two tall pea plants sometimes also produced short pea plants. A model of blending inheritance cannot explain recessive traits, but a Mendelian framework can. Whereas intuitive blendings of inheritance take the visible traits as the only variables of interest in understanding intergenerational change in characteristics, Mendelian genetics implies that phenotypes emerge from the interactions of underlying genotypes.</p>
<p>These genotypes are the true factors through which variation is preserved from generation to generation; an organism’s visible characteristics are only pointers to the true underlying heritable variation present in the genes. Darwin’s <em>Origin of Species </em>was published in 1859 to great fanfare, but Darwin famously lacked a plausible mechanism of inheritance that could maintain the variation that was necessary for natural selection. Mendel provided the answer, but the Austrian monk’s single 1866 paper, “Experiments on Plant Hybridization,” was ignored by the scientific community of the time, only to be rediscovered around 1900, when the modern field of genetics was born.</p>
<p>But twentieth-century genetics very much worked within Gregor Mendel’s methodological framework. Genes were analytical units, abstractions necessary to explain the patterns of inheritance visible in breeding experiments, but not understood in physical terms. Genetics proceeded through analyses of patterns of inheritance in pedigrees and populations, a laborious matter of inspection and inference. The journey to where we are today, when we can read out the sequence of any organism that we choose, began in the 1940s when biologists realized nucleic acids were the medium through which genetic information was transmitted.</p>
<p>After James Watson and Francis Crick’s elucidation of the structure of DNA in 1953, the molecular biological revolution that it ushered in allowed geneticists to conceive of the idea of mapping genes in a direct physical manner, rather than inferring them through the transmission of phenotypes within pedigrees. But even <a href="https://www.nytimes.com/1975/09/14/archives/scientists-now-can-make-human-genetic-maps.html" rel="">as late as 1975</a> only one hundred genetic positions were mapped in the human genome across all populations. The first complete biophysical genetic map of an organism, <em>Haemophilus influenzae</em>, was published in 1995 with a1.83 million base pair length sequence. By 2020 there were tens of thousands of different species sequenced. The story of the mutation of genetics from a data-poor to a data-rich science is one of exponential technological change; it is very much a synergy between rapid advances in <a href="https://www.techtarget.com/searchdatacenter/definition/parallel-processing#:~:text=Parallel%20processing%20is%20a%20method,parts%20of%20an%20overall%20task." rel="">computing</a> and novel <a href="https://www.genome.gov/genetics-glossary/Polymerase-Chain-Reaction" rel="">innovations</a> in chemistry.</p>
<p>But more interesting than the exponential growth in data are the surprising things we have inferred from the data. In the heady early days of the publication of the draft of the human genome over twenty years ago, co-author Francis Collins asserted that the combination of molecular biology and genomics would “make a significant impact” on our attempt to understand and cure cancer. Despite some early instances where genomic sequencing was performed on cancer patients, like Steve Jobs in 2009, the overall impact of the new science on healthcare has been modest at best. Instead, paleoanthropology, prehistory, and history were transformed as genetics surveyed the pedigrees of the human past with a power and precision that would have been unimaginable a generation ago.</p>
<p>Even though the Swedish geneticist Svante Pääbo published a paper in 1984 on the DNA of mummies, pioneering the field that would become paleogenomics, it is clear that much of his work in the 1980s and early 1990s was simply reporting sample contamination; the DNA detected was that of lab workers or people who had handled artifacts and specimens. But in 2022, Pääbo was awarded the Nobel Prize in Physiology and Medicine for the transformative work that began in the 2000s. He and his colleagues had learned from earlier errors, and taken to the new genomic technology with gusto.</p>
<figure id="attachment_6790" aria-describedby="caption-attachment-6790" style="width: 1024px" class="wp-caption aligncenter"><img loading="lazy" decoding="async" class="size-large wp-image-6790" src="https://pdmedia.b-cdn.net/2023/11/e757b3f3-989b-49dc-bfdd-72e0d41a5cb4_1600x1200-1024x768.jpg" alt="" width="1024" height="768" srcset="https://pdmedia.b-cdn.net/2023/11/e757b3f3-989b-49dc-bfdd-72e0d41a5cb4_1600x1200-300x225.jpg 300w, https://pdmedia.b-cdn.net/2023/11/QCK9rPTS-e757b3f3-989b-49dc-bfdd-72e0d41a5cb4_1600x1200-1024x768.jpg 1024w, https://pdmedia.b-cdn.net/2023/11/e757b3f3-989b-49dc-bfdd-72e0d41a5cb4_1600x1200-768x576.jpg 768w, https://pdmedia.b-cdn.net/2023/11/e757b3f3-989b-49dc-bfdd-72e0d41a5cb4_1600x1200-1536x1152.jpg 1536w, https://pdmedia.b-cdn.net/2023/11/e757b3f3-989b-49dc-bfdd-72e0d41a5cb4_1600x1200-450x338.jpg 450w, https://pdmedia.b-cdn.net/2023/11/e757b3f3-989b-49dc-bfdd-72e0d41a5cb4_1600x1200-800x600.jpg 800w, https://pdmedia.b-cdn.net/2023/11/e757b3f3-989b-49dc-bfdd-72e0d41a5cb4_1600x1200.jpg 1600w" sizes="auto, (max-width: 1024px) 100vw, 1024px" /><figcaption id="caption-attachment-6790" class="wp-caption-text">Demin Barnaul/Denisova cave in Siberia, which was inhabited by Neanderthals, Denisovans and modern humans, and their mixed progeny.</figcaption></figure>
<p><span style="font-size: 1em; letter-spacing: 0px;">The first modern human genetic map was published one hundred years after the founding of the field, but the first prehistoric human genetic map was published ten years after that, when Pääbo’s group released the draft of the Neanderthal genome in May 2010. The team then unveiled the genome of a new human species, Denisovans. Named after the Denisova cave in Siberia, where a broken finger bone and a single molar yielded their genome, they are a whole additional branch of humanity distinct from but closer to Neanderthals than modern humans. While Neanderthals are well-known from paleontology and archaeology, Denisovans were novel because they have been identified only from their distinct genetic markers. Genomics was resurrecting the DNA of literally vanished species of humans that were totally unknown to science.</span></p>
<h3>Humanity Was Once Not One Species, But Many</h3>
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<p>DNA is a robust macromolecule, a feature that is useful in maintaining high information fidelity across generations. The rate at which it degrades can vary significantly depending on several factors, including the surrounding environment, temperature, and the presence of water or enzymes. But DNA is a stable enough molecule that it can easily persist for thousands of years under favorable conditions and, in some rare cases, over one million years.</p>
<p>Svante Pääbo’s esteem in the field of science owes much to the punctilious processes that he has pioneered for the analysis of ancient DNA preserved in the teeth and bones of subfossils. The task is not trivial due to contamination, but paleogeneticists have now perfected the techniques well enough that, where a generation ago sequencing a single human genome was a massive achievement, today we have <a href="https://www.nature.com/articles/d41586-023-01403-4" rel="">more</a> than 10,000 ancient human genomes.</p>
<p>More interesting to the general public than the biophysics of DNA preservation is the information that we can obtain from DNA. In the 20th century, geneticists used the variation of modern people to make inferences about the past, most famously with the “Out of Africa” theory of the origin of our species. In the 21st century, paleogeneticists don’t just reconstruct the tree of life, they actually expose its nodes, branches, and roots by obtaining ancient DNA. This fine-grained, detailed map of the human past allows for extremely precise conclusions to be drawn about general human demographics and social structure.</p>
<p>Even a single high-quality genome is informative because the three billion base pairs and millions of variants that convey unique individual information reflect the sum totality of a population’s history by ascending backward in their genealogy. The variation of the entire genome sequence of a single human makes it clear our lineage went through a bottleneck in the last 100,000 years, and that we’ve undergone massive population growth in the last ten thousand years. Similarly, the genome of a single Neanderthal also tells us that this lineage, unlike our own, seems to have existed at very low population numbers throughout its history.</p>
<p>Today, we know that Neanderthals varied in hair color, just like modern humans, and that their genome was 99% identical to those of our own lineage. They were physically more robust, which is clear from their fossils, and their genes for bone development and muscle development differ from ours. And, to the surprise of geneticists thirteen years ago, it was also clear that most modern humans have some Neanderthal ancestry. Outside of Africa, the figure is between 2% and 2.5%, and it is present from Australia to Ireland. The implication is that early on in the modern human expansion out of Africa they mixed with a group of Middle Eastern Neanderthals.</p>
<p>This shocking result only came out through ancient DNA. Not only do modern humans have Neanderthal ancestry, but some of us have Denisovan ancestry. It comprises 5% of the heritage of Papuans and lower fractions of Denisovan ancestry are found throughout Asia. There is an open question in anthropology as to whether humans are naturally promiscuous. The data from DNA shows that our forebears were sexually open to liaisons with populations and people quite different from them, and definitely forces us to lean in one direction in the debate.</p>
<p>Using a genomic clock, ‌Neanderthals and modern humans became separated 600,000 years ago. The most distinct lineage in modern populations, between South African Khoisan and all other humans, clocks in at 200,000 years. Our ancestors’ sexual preferences were evidently very broad. In a cave in Russia, Researchers have even discovered a young girl whose mother was a Neanderthal and whose father was a Denisovan. Statistically, the probability of catching a first-generation hybrid is low; the fact that it was discovered shows that this behavior was common.</p>
<p>But did the Denisovans and Neanderthals disappear into the loving arms of humans migrating out of Africa, or was there capture and coercion involved? The data to answer this question does not exist for these early encounters, but is more copious for later prehistoric epochs. Premodern humans clearly made love, but they also made war. Earlier generations of paleoanthropologists believed that modern populations descend from groups that diverged and settled down 50,000 years ago and turned into what we now know as regional populations: Europeans, Africans, East Asians, and South Asians. The ancestors of modern Europeans were thought to be the Cro-Magnons that arrived 45,000 years ago and replaced the Neanderthals.</p>
<p>Ancient DNA and genomics make it clear that this idea is wrong. The Cro-Magnons left no descendants; they’re totally unrelated to other modern populations. Rather, about 38,000 years ago, they were replaced by another group of humans from the southeast who eventually gave rise to the Gravettian culture, notable for producing small ivory sculptures. Then, 20,000 years ago, another culture arrived that gave rise to the cave-painting Magdalenians, replacing the earlier populations. Then, 15,000 years ago, more waves of foragers migrated out from the Middle East, again mostly replacing the earlier populations.</p>
<p>Farmers arrived 8000 years ago with the Neolithic Revolution, only to be replaced 4500 years ago by Indo-Europeans from the steppe. The story of Europe is the story of the world; humans are always on the move, and one group replaces another, over and over. Unlike many other organisms, humans are not sessile and geographically concentrated. Our demographic equilibrium is inevitably shocked by radical transformations. For modern humans, all is change.</p>
<h3>The Genghis Khan Effect and Population Replacement</h3>
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<p>How did humans replace other humans? The evidence from ancient DNA in Europe sheds light on the structure of these early societies. The great longhouses of Neolithic Germany were ruled by groups of men who were related, sharing the same Y-chromosomal lineage. The women, in contrast, were strangers, judging by their diverse maternal lineages. When Indo-Europeans arrived 4500 years ago, the ancient DNA record shows a total turnover of Y chromosomes, with the older lineages replaced by new ones. In contrast, the maternal lineages show continuity. In genetic parlance, this is “male-mediated migration,” but ‌it was probably quite like the Spanish conquest of the New World, with young males taking new lands and women by force.</p>
<p>The Roman recollection of the rape of the Sabine women likely reflects cultural memory of events in prehistory, where victorious males obtained mates from the lands they conquered after killing the fathers and brothers of the women they would make wives. Prehistoric human males behaved like lions taking over a pack, killing everyone among the conquered except for nubile females. Genetics shows that since the end of the last Ice Age, paternal lineages are characterized by periodic explosions, where one clan seems to have replaced all the others through a process of competition and polygyny.</p>
<p>Call it the “Genghis Khan effect,” but the Mongolian world emperor was simply the last in a long line of “super-males” that have defined much of the last 12,000 years. They say to believe them when they tell you who they are, and the legends of the Indo-Europeans reflect a patriarchal and warlike culture, destroyers of cities like the god Indra and near-immortal warriors like Achilles, and this is exactly what genetics tell us about them. In prehistoric Sweden, the Neolithic Megalith builders who dominated the region for more than 1000 years seem to have been totally exterminated by the invading “Battle-Axe” culture. The development of agriculture was a new technology that allowed for the expansion of human societies and the emergence of social stratification, but combined with our innate instincts, genetics make it clear that the drive to extermination manifested itself in most places and most times.</p>
<p>We cannot avoid what human nature was for tens of thousands of years in the past. It was bloody, it was brutal, and it was typified by genocide. This is the legacy we inherit, but it is not the legacy we need to replicate. The average life expectancy in the past was also much shorter than in the present, but the application of technology and social institutions has ameliorated the toll that disease takes on the human body. Human societies are also organisms and their rise and fall are measured in the waves of change in the genes of our own species. To the victors go the spoils and the seeds of the future. But institutions like monogamy and a modicum of wealth redistribution can be thought of as social technologies that dampen the volatility inherent in human relationships, a volatility that can manifest in chaos and warfare. Not a war of all against all, but a war where winners took all.</p>
<h3>The Hero Prometheus Unchains the God Asclepius</h3>
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<p>If the application of genomics to understanding our past is the present, then the application of genomics to medicine will be our future. The original value proposition of the Human Genome Project was in medical health, and overall genomics has not lived up to the early hype. The reason turns out partly to be that the architecture of the genetics of diseases was not what we had assumed twenty years ago. Instead of a few mutations that have an outsized impact, conditions like type 2 diabetes, schizophrenia, and cancer are defined by numerous genes that cause a person to be at risk.</p>
<p>A single entire genome—or a few hundred—was only the start. These were necessary preconditions to understand diseases, but not sufficient. Today, we know that most diseases are complex or polygenic, because of the action of hundreds or thousands of genes, and many of the causal mutations are quite rare. Human variation is substantial enough that generalizations across individuals have limited utility until reaching the very large sample sizes that are only feasible today. The value of genomics is thus directly proportional to the number of genomes sequenced. This means that the true promises of genomic health will only come to the fore in the next decade, as we scale sample sizes to new heights.</p>
<p>The lowest hanging fruit for genetic health is for single-gene Mendelian disorders. In the 1990s, detecting the mutations for diseases like cystic fibrosis was worthy of coverage in the pages of <em>The New York Times</em>. Today, most of these diseases have been characterized in terms of their mutations, and diagnostic services are available in developed countries. The power of genomics to find unknown unknowns is illustrated most powerfully already in the pediatric domain. Newborns who are born and do not flourish are now habitually sequenced and, currently, disorders can be identified immediately in 40% of cases.</p>
<p>When technology becomes ubiquitous, it becomes not worth mentioning; already millions of women take for granted noninvasive prenatal tests that detect whether a fetus has Down’s syndrome or other chromosomal abnormalities. These tests have allowed for the phasing out of amniocentesis after 2015, and in the future, their power will increase. They operate by extracting the genetic signal of the fetus from the blood sample drawn from the mother; complex computational algorithms that distinguish the faint signal of fetal cells that are present in the pregnant woman.</p>
<p>Next up after the detection of chromosomal abnormalities will be Mendelian diseases like Tay-Sachs disease, cystic fibrosis, and sickle cell disease. But in the next twenty years, these prenatal methods will expand to highly heritable complex diseases: autism is 85% heritable, Alzheimer’s risk is 70% heritable, schizophrenia is over 75% heritable, and bipolar disorder is 70% heritable. The implication here is clear: we can eliminate many of these diseases through genetic screening of embryos or selective termination. The problem may be that some of these characteristics, like schizophrenia, are also associated with creativity. If we improve our gene pool, are we throwing the baby out with the bathwater?</p>
<p>The age of ubiquitous reading of the genome is around the corner. The technology is orders of magnitude cheaper and more efficient than even a decade ago. By the 2030s, we’ll have near-zero-cost sequencing, and it won’t require a massive machine. Instead, imagine portable kits that you could carry and can perform high-scale computation on your desktop or in your pocket. And the spread of computation into everyday life will include genomics. One of the most essential monitors of your own health will likely be the toilet, which will get samples of your cells and your microbiome several times a day.</p>
<p>Rather than unnatural and intrusive medical tests, monitoring will embed itself in our lives, and genomics will be a large part of it because of the plasticity and mutability of your sequence over your life through variation in gene expression. One reason that pancreatic cancer is so fatal is that it is detected only late in life. Imagine a scenario where your toilet is constantly sampling the cells that you shed and is able to detect mutations and abnormalities once they rise above the threshold of salience.</p>
<p>But the age of reading will soon be joined by the age of editing. Genetics is a science of retrospective analysis, but it is also a science of application, colloquially known as “genetic engineering.” The tools and techniques of genetic engineering have been available since the 1970s, but in 2012 CRISPR technology allowed for a quantum leap in the ease of methodology, as well as accuracy and precision. If previous recombinant DNA technologies were a buzzsaw, CRISPR editing is like a paring knife. A decade out, CRISPR has been applied to only a few cases, like curing <a href="https://www.npr.org/sections/health-shots/2021/12/31/1067400512/first-sickle-cell-patient-treated-with-crispr-gene-editing-still-thriving" rel="">sickle cell</a>.</p>
<p>As with any technology, it is still imperfect and not suitable for the treatment of most diseases due to the risk of the introduction of novel mutations that might cause diseases like cancer. But the rate of change is such that it is clear that genetic engineering will be safe and affordable within a generation, and that is when the true implications of the genetic revolution will confront us. Instead of simply reading the book of life, we will have the ability to write it. The question will not be about our ability to do something, but our willingness. What had previously been technical questions will become normative ones.</p>
<h3>We Will Either Evolve or Go Extinct</h3>
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<p>The twentieth century saw humanity’s grasping of Promethean powers in the realm of physics. Nuclear weapons have the potential either to power or to destroy our civilization. But unlike the rise of agriculture, this new technology did not in fact unleash a bloodbath—so far at least. The emergence of international institutions and the aversion to using nuclear weapons by international elites ushered in an era of relative peace, at least compared to the wars of the first half of the twentieth century. Genetics has made it clear that the rise of civilization was soaked in blood, but nuclear technology is a case in point that awesome powers do not always entail doom.</p>
<p>The 21st century will see massive developments in biology analogous to nuclear weapons. Since the emergence of this scientific field out of anatomy and natural history in the 19th century, the focus has been on understanding and reflection, rather than direct application. There are exceptions, like the multi-decade gain in lifespan in the mid-20th century for children with type 1 diabetes, as well as the spread of vaccination and antibiotics. Both vaccination and antibiotics co-opt nature, but the production of insulin was one of the first successes of recombinant DNA technology.</p>
<p>Insulin is produced by bacteria that have been genetically engineered with human biochemical pathways. Within one generation, it seems likely that instead of using genetic engineering to create biological products for humans, the tools will be powerful enough that we can recreate and re-fashion ourselves at the level of our genetic blueprint. The question is not whether we can do it, the question is whether we will or even should. Will humanity remake itself in whatever image it chooses? Or will it bow down before the mandate of nature’s law?</p>
<p>The human propensity for competition and domination was a toxic cocktail when mixed with the new technologies of agriculture; foraging tribes scaled up simply expanded the horizon of brutality. It is almost inevitable that the age of eugenics will arrive in the near future. In the science fiction treatment of <em>Star Trek</em>,genetic modifications unleashed a sect of supermen upon the world, triggering the “Eugenics Wars.” This is one vision of the future, where genetic enhancement unlocks our capacity for brutality, taking it to the next level, just as agriculture seems to have.</p>
<p>But there is another possibility: that we can and should modify our personalities, our natures, to make us somewhat less the “Pleistocene mind” trapped in a technological world. Genomic technologies have made it crystal clear how our forager mindsets can take society down dark turns in the face of new technological opportunities; we now have the technology to remake humanity by tinkering with the biomolecular machinery and making us more adept and fitting for the glittering world that we inhabit.</p>
<div class="author-bio">
<p class="author-description">Razib Khan is a co-founder <a href="https://www.genrait.com/">GenRAIT</a>, a deep tech company that deploys a platform for the life sciences. He also writes at Razib Khan’s <a href="https://www.razibkhan.com/">Unsupervised Learning</a>. You can follow him at <a href="https://twitter.com/razibkhan">@razibkhan</a>.</p>
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