Razib Khan's Unsupervised Learning

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Bonus monologue: man the hybrid monster
Today, Razib talks about a new paper, A structured coalescent model reveals deep ancestral structure shared by all modern humans: Understanding the history of admixture events and population size changes leading to modern humans is central to human evolutionary genetics. Here we introduce a coalescence-based hidden Markov model, cobraa, that explicitly represents an ancestral population split and rejoin, and demonstrate its application on simulated and real data across multiple species. Using cobraa, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ~1.5 million years ago came together in an admixture event ~300 thousand years ago, in a ratio of ~80:20%. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human–Neanderthal or human–Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.
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19:35
John Sailer: a time of troubles in higher education
On this episode of the podcast Razib talks to John Sailer. Sailer is currently the director of higher education policy and a senior fellow at the Manhattan Institute. He covers issues of academic freedom, free speech, and ideological capture in higher education. Sailer has written for the Wall Street Journal, the Free Press and Tablet Magazine. Sailer holds a master’s degree in philosophy and education from Columbia University, and a bachelor’s degree in politics, philosophy, and economics from The King’s College. Prior to joining the Manhattan Institute, he was a senior fellow at the National Association of Scholars. Following on last week’s podcast with Jacob Shell, Razib continues to discuss the rise and fall of woke politics in academia, and the current backlash exploding out of the Trump administration. Sailer discusses his previous work back to 2020 showing how blatant universities became in their discriminatory policies against white males in particular, and how easy it was to demonstrate this dynamic with even the most minimal level of due diligence like freedom of information requests. They also discuss the reality that universities are attempting to adjust to a new landscape with the administration pressuring them to revoke DEI policies, while many faculty are urging that they instead dig in their heels. Higher education is adapting, but Sailer argues that since fundamental values have not changed, some evasion is to be expected.
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1:22:25
Jacob Shell: academia must diversify or die
On this episode of Unsupervised Learning Razib talks to Jacob Shell. Shell is a professor of geography at Temple University and author of Transportation and Revolt: Pigeons, Mules, Canals, and the Giants of the Monsoon Forest: Living and Working with Elephants. Educated at Columbia and Syracuse universities, Shell is active on social media, where he comments extensively on the politicization of the academy. The conversation begins with Shell’s piece in Compact Magazine, To Save Academia, Hire Conservatives. The more than 3,000-word essay argues that academia must diversify ideologically to save itself, but also engage in a wider range of scholarship. Shell points out that US academia has become an ideological monoculture, with an overwhelming dominance of left-leaning faculty, especially at elite institutions. This imbalance, driven by extreme partisan ratios in fields like anthropology, leaves universities politically vulnerable and out of step with the broader public. He challenges the common view that this trend is due to self-selection, or the “pipeline problem,” suggesting instead that informal screening mechanisms discourage or exclude conservative scholars. Shell also argues that the grant system encourages conformity and limits academic freedom. More audaciously, he argues that some academics should be singled out by their peers, whether through their institution or professional organizations,t when they engage in politically motivated misrepresentation of their scholarship. Ultimately, Shell insists that academia’s unique role in public life is to observe and understand the world, not to risk co-option as an arm of any political movement.
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1:43:54
Matt Welch: from blog pioneer to podcasting mainstay
On this episode of Unsupervised Learning Razib talks to Matt Welch. He co-founded the Prague-based newspaper Prognosis in the early 1990’s and later worked as an opinion section editor for the Los Angeles Times. From 2008-2016, Welch served as editor-in-chief of Reason magazine, where he currently holds the position of editor-at-large. He co-authored The Declaration of Independents: How Libertarian Politics Can Fix What's Wrong with America and wrote McCain: The Myth of a Maverick. Today, Welch co-hosts The Fifth Column podcast with Kmele Foster and Michael Moynihan. Razib and Welch first go back to his days in Eastern Europe, and how they shaped his views on foreign policy, making him somewhat heterodox for someone whose primary political inclinations favor libertarianism. Welch discusses how wild, hopeful and chaotic the 1990’s were in the former Eastern Bloc after the fall of the Iron Curtain and the end of Communism. He also argues that these nations had strong historic and contemporary geopolitical reasons to fear the former Soviet Union, and so pushed for the eastward expansion of NATO. Razib makes the Russian case that its turn away from the West in the 2000’s was in response to America’s strategy of encirclement, but Welch dismisses this as Russian revisionism. He believes that at the end of the day Soviet-era elites retained an imperial attitude toward Eastern and Central Europe rooted in a centuries-long assumption of Russian hegemonic status in the region. Next, retreating from abstruse foreign policy, Razib and Welch discuss the early days of the blogosphere, in 2001/2002. Then, Welch coined the term “warblogger,” and envisaged a scenario where post-partisan citizen-journalists would play an essential role in the information ecosystem of the 21st century. He discusses his disappointment with the reemergence of partisanship within the blogosphere, as well as the disappointments of post-9/11 interventionism. Welch also talks about the Tea Party, and its connection, and ultimate disconnect, from libertarianism. They also discuss how the Tea Party energy was eventually transferred to the ideologically heterodox and often anti-libertarian Trump movement. Finally, Welch talks about his latest primary venture, the successful The Fifth Column podcast. Razib asks if the current age of podcasting is analogous to the early blogosphere. Welch talks about how organically and gradually The Fifth Column came into being, and the growing pains with greater professionalization. He also addresses their future on The Fifth Column, with a new shift toward video, while continuing the informal and candid nature of the discussions.
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1:28:10
Bonus monologue: ancient North Africans and the Green Sahara
On this episode of Unsupervised Learning Razib comments on a new paper in Nature, Ancient DNA from the Green Sahara reveals ancestral North African lineage. Here is the abstract: Although it is one of the most arid regions today, the Sahara Desert was a green savannah during the African Humid Period (AHP) between 14,500 and 5,000 years before present, with water bodies promoting human occupation and the spread of pastoralism in the middle Holocene epoch1. DNA rarely preserves well in this region, limiting knowledge of the Sahara’s genetic history and demographic past. Here we report ancient genomic data from the Central Sahara, obtained from two approximately 7,000-year-old Pastoral Neolithic female individuals buried in the Takarkori rock shelter in southwestern Libya. The majority of Takarkori individuals’ ancestry stems from a previously unknown North African genetic lineage that diverged from sub-Saharan African lineages around the same time as present-day humans outside Africa and remained isolated throughout most of its existence. Both Takarkori individuals are closely related to ancestry first documented in 15,000-year-old foragers from Taforalt Cave, Morocco2, associated with the Iberomaurusian lithic industry and predating the AHP. Takarkori and Iberomaurusian-associated individuals are equally distantly related to sub-Saharan lineages, suggesting limited gene flow from sub-Saharan to Northern Africa during the AHP. In contrast to Taforalt individuals, who have half the Neanderthal admixture of non-Africans, Takarkori shows ten times less Neanderthal ancestry than Levantine farmers, yet significantly more than contemporary sub-Saharan genomes. Our findings suggest that pastoralism spread through cultural diffusion into a deeply divergent, isolated North African lineage that had probably been widespread in Northern Africa during the late Pleistocene epoch.
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18:12