Articles d'hiver intéressants

[Adrian]

Concepts: race and genetic ancestry

 

Citation

• Race and genetic ancestry are distinct concepts with distinct causes and consequences. Race is defined within a social context. Genetic ancestry is defined within the context of reference populations.
• Race, either a historical “essentialist” views or a more contemporary “population” views, provides a poor model of true genetic variation. Genetic variation follows a “nested subset” model where the most variation is observed in Africa and subsets of that variation are observed in Europe, Asia, and the Americas. Model fitting of race to genetic data provides a much worse fit than a nested subset model that is incompatible with race (Long, Li, and Healy 2009).
• Comparing pairs of sequenced individuals, the largest number of differing sites were within Africa (consistent with a nested evolutionary model): a pair of Yoruba/Yoruba individuals have more differences than a pair of Yoruba/French individuals (Biddanda, Rice, and Novembre 2020). Most of the differences between pairs of individuals were because one individual carried a globally common allele and the other did not.
• Estimates of FST between divergent geographic populations range between 0.11 and 0.15 (Bhatia et al. 2013), in other words, if we take the individual-level genetic variation at a typical polymorphism and condition out population labels, we will still be left with 85% of the original variance. This is in stark contrast to historic racial models that assumed racial groups were largely homozygous within populations and highly divergent between (i.e. FST close to 1.0).
• A brief tour of methods for analyzing population structure in genetic data:

1. Principal Components Analysis (PCA), an eigendecomposition of the sample relatedness matrix, can identify individuals drawn from populations with differing allele frequencies. Theory indicates that PCA is extremely sensitive and is expected to identify structure in most large datasets (Patterson, Price, and Reich 2006). While PCA has useful genealogical properties, it is easily distorted by the sampling of individuals (McVean 2009) and can also produce arbitrary non-linearities in the presence of spatially local structure (Novembre and Stephens 2008).
2. Model-based clustering (STRUCTURE) attempts to identify individuals as mixtures of alleles from a fixed set of populations (Pritchard, Stephens, and Donnelly 2000). STRUCTURE is similarly distorted by the sampling of individuals, as well as the number of defined populations, including identifying admixtures that do not exist in truth or missing admixtures that do exist (Lawson, van Dorp, and Falush 2018).
3. Parametric models (Admixture Graphs) attempt to fit populations to trees or graphs based on tests of cross-population allele sharing. Admixture graphs can often identify incorrect graphs that provide a better fit to the data than the true graph, or many equally likely graphs. Reanalysis of published admixture graph studies demonstrated several instances where historical conclusions were drawn from data that was compatible with many different graphs (Maier et al. 2023).
4. All ancestry inference methods are biased by the sampling process and/or model parameters, and no method can identify “true” ancestry because the true sampling process is unknown.

• A brief tour of genetic ancestry in large-scale datasets:

1. All large biobanks exhibit continuous population structure that is poorly explained by conventional racial groups (Wojcik et al. 2019).
2. When restricting to “homogenous” ancestry populations enriched for European origin, continuous PCs are observed that reflect ancestry from reference populations within Europe (Galinsky et al. 2016). When restricting to homogenous white individuals in a single European country (the UK), county level PCs are observed (Agrawal et al. 2020).
3. The same patterns arise in other countries: A large Chinese biobank identified PCs that correlated with within-city neighborhoods (Walters et al. 2023); a large Japanese biobank identified PCs that correlated with dozens of local regions (Sakaue et al. 2020).

• A brief tour of human history from population genetics:

1. Diverse studies of modern and ancient DNA have demonstrated that historic admixtures and migrations were ubiquitous and highly dynamic. Genetic ancestry rarely reflects current geographic patterns and disputes simple models of isolated human development (Pickrell and Reich 2014).
2. Modern individuals from the Americas are generally more similar in their ancestry to European than to Native American reference individuals (Moreno-Estrada et al. 2013; Gravel et al. 2013). Native American reference individuals exhibit complex relationships to ancient Siberian genomes as well as modern Polynesian populations (Ioannidis et al. 2020), where the latter appear to have been settled directly by East Asian groups (Skoglund et al. 2016).
3. European individuals derive ancestry from historic populations that often no longer exist in un-admixed form (Lazaridis et al. 2014; Sikora et al. 2019) or were rapidly displaced (Olalde et al. 2018). In more recent history (the Bronze Age) both extensive migration and population structure have been observed across Europe (Antonio et al. 2024).
4. Admixture and migration is extensive in Africa in both modern (Fan et al. 2023) and ancient data (Skoglund et al. 2017; Lipson et al. 2020). Yet there are massive gaps in our understanding of African population history including competing theories of continuously mixing pan-African “metapopulations” (Scerri, Chikhi, and Thomas 2019; Ragsdale et al. 2023) versus recent “back to Africa” migrations (Cole et al. 2020).

• In short, human history has been highly dynamic, with extensive admixture, instances of rapid migration, geographic shifts, ancient introgression events, historic populations that no longer exist in unadmixed forms. Conventional models of race are irrelevant to the study of genetic variation, and even models of simple population relationships are proving to be fundamentally wrong.

 

@Rincevent, summary

[Sloonz]

Il manque peut-être un thread "tweets intéressants" ?

 

https://twitter.com/Devon_Eriksen_/status/1847651018542096726

 

[Rübezahl]

Très bon tweet, merci. Mais perso un rangement thématique dans un fil existant me paraît mieux qu'un thread fourre-tout de bon tweets.

[Rincevent]

Il y a 10 heures, Adrian a dit :

Conventional models of race are irrelevant to the study of genetic variation

Bah, ouais ; placer les Igbos et les Mbuti dans la même catégorie "congoïde" (coucou Riton), c'est un indice fort que classer les origines ethniques en cinq "races" manque singulièrement de résolution pour la plupart des applications.

 

Il y a 10 heures, Adrian a dit :

Admixture and migration is extensive in Africa

"Africa", ça manque aussi singulièrement de résolution. Pour rappel, les Khoisan ont vécu génétiquement isolés du reste de l'espèce humaine pendant plusieurs dizaines de milliers d'années.

[Adrian]

'Dysgenic fertility' is an ideological, not a scientific, concept. A Comment on: ‘Stability and change in male fertility patterns by cognitive ability across 32 birth cohorts’ (2023), by Bratsberg & Rogeberg

[Rincevent]

Il y a 8 heures, Adrian a dit :

'Dysgenic fertility' is an ideological, not a scientific, concept. A Comment on: ‘Stability and change in male fertility patterns by cognitive ability across 32 birth cohorts’ (2023), by Bratsberg & Rogeberg

[Hugh]

Une entrevue de Trotsky par Simenon:

 

https://www.marxists.org/francais/trotsky/oeuvres/1933/06/ldt19330607.htm (badurl)

 

C'est beaucoup pour poster tout, mais le commence:

 

Citation

J'ai rencontré dix fois Hitler, au Kaiserhof, alors que, tendu et fébrile, déjà chancelier, il menait sa campagne électorale. J'ai vu Mussolini contempler sans lassitude le défilé de milliers de jeunes hommes. Et à Montparnasse, un soir, j'ai reconnu Gandhi dans une silhouette blanche qui rasait les maisons, suivie par de jeunes femmes fanatiques.

 

Pour avoir une entrevue avec Trotsky, me voilà sur le pont plus grouillant que le Pont-Neuf de Paris qui relie le vieux et l'ancien Constantinople, Stamboul et Galata. Pourquoi vais-je avoir désormais une impression de beau dimanche sur la Seine, du côté de Saint-Cloud, de Bougival ou de Poissy ? Je n'en sais rien.

 

Tous les bateaux, autour des embarcadères enchevêtrés, me font penser à des bateaux-mouches. Ils sont plus grands ? C'est certain. Ils ont même un petit air marin et l'hélice bat de l'eau salée. Mais c'est une question de proportion. C'est tout le décor qui est plus vaste, le ciel lui-même plus lointain.

 

Ici, une rive s'appelle l'Europe et l'autre l'Asie. Au lieu des remorqueurs et des péniches de la Seine, ce sont autant de cargos et de paquebots qui battent pavillon de tous les pays du monde, s'en vont vers la mer Noire ou se faufilent dans les Dardanelles.

 

Qu'importe ? Je garde mon impression de beau dimanche, de banlieue, de guinguettes. Il y a des couples d'amoureux sur le pont du bateau, des paysans qui transportent des poules et des coqs dans des cages, des marins en permission qui sourient d'avance au plaisir qu'ils vont se donner.

 

Trotsky ? Je lui ai écrit avant-hier pour lui demander une entrevue. Le lendemain matin déjà j'étais réveillé par la sonnerie du téléphone.

 

[Adrian]

Wikipedia : Orthographies and dyslexia

 

Citation

The complexity of a language's orthography is directly related to the difficulty of learning to read in that language. Orthographic complexity also contributes to how dyslexia manifests in readers of different languages.^[14]

 

Deep orthographies are writing systems, such as those of English and Arabic, that do not have a one-to-one correspondence between sounds (phonemes) and the letters (graphemes) that represent them.
 

Shallow orthographies, such as Italian and Finnish, have a close relationship between graphemes and phonemes, and the spelling of words is very consistent. With shallow orthographies, new readers have few problems learning to decode words and as a result children learn to read relatively quickly. Most dyslexic readers of shallow orthographic systems learn to decode words with relative ease compared to dyslexics using deep orthographies, though they continue to have difficulty with reading fluency and comprehension.^[8] The hallmark system of dyslexia in a shallow orthography is a comparatively slow speed of rapid automatized naming.
 

For languages with relatively deep orthographies, such as English and French, readers have greater difficulty learning to decode new words than languages with shallow orthographies. As a result, children's reading achievement levels are lower.^[15] Research has shown that the hallmark symptoms of dyslexia in a deep orthography are a deficit in phonological awareness and difficulty reading words at grade level.^[16] For these dyslexic readers, learning to decode words may take a long time—indeed, in the deepest orthographies a distinctive symptom of dyslexia is the inability to read at the word level—but many dyslexic readers have fewer problems with fluency and comprehension once some level of decoding has been mastered.

[...]
there is little evidence that a more "regular" orthographic system would significantly diminish the number of dyslexia cases. Because there is also a visual aspect to dyslexia, affected children often show symptoms such as mirror letter reversal (e.g. confusing "b" and "d"), which can manifest in any language regardless of orthographic depth.)

 

[Bisounours]

Article-témoignage intéressant dans le sens où il cumule tous les clichés de gauche. Il est tiré du livre L'argent des gens de Thomas Baumgartner (ça commence fort) qui regroupe dix témoignages sur le rapport à l'argent.

 

Au fur et à mesure de cette lecture crispante, l'envie augmente de botter l'arrière-train de cette pauvre victime (de ses choix foireux) :

"Après deux premières années d'histoire, j'ai fait une fac d'arts du spectacle. Je pratiquais le théâtre depuis quelques années"

 

C'est un festival.

 

 

[Lancelot]

C'est interminable et répétitif.

 

Quote

Je ne me considère pas comme étant de la classe ouvrière.

Non tu fais partie de la classe parasite cassos. Pas de quoi être fière. Les ouvriers au moins ils produisent quelque chose même si tu les méprises.

[Bisounours]

il y a 5 minutes, Lancelot a dit :

C'est interminable et répétitif

Carrément. Son témoignage aurait pu se résumer en quelques lignes. Si tout le livre est de cet acabit, quelle purge nullissime.