A review of intelligence GWAS hits: Their relationship to country IQ and the issue of spatial autocorrelation

Typological thinking in human genomics research contributes to the production and prominence of scientific racism

Public genomic datasets like the 1000 Genomes project (1KGP), Human Genome Diversity Project (HGDP), and the Adolescent Brain Cognitive Development (ABCD) study are valuable public resources that facilitate scientific advancements in biology and enhance the scientific and economic impact of federally funded research projects. Regrettably, these datasets have often been developed and studied in ways that propagate outdated racialized and typological thinking, leading to fallacious reasoning among some readers that social and health disparities among the so-called races are due in part to innate biological differences between them. We highlight how this framing has set the stage for the racist exploitation of these datasets in two ways: First, we discuss the use of public biomedical datasets in studies that claim support for innate genetic differences in intelligence and other social outcomes between the groups identified as races. We further highlight recent instances of this which involve unauthorized access, use, and dissemination of public datasets. Second, we discuss the memification, use of simple figures meant for quick dissemination among lay audiences, of population genetic data to argue for a biological basis for purported human racial groups. We close with recommendations for scientists, to preempt the exploitation and misuse of their data, and for funding agencies, to better enforce violations of data use agreements.

Why are there differences across German states in student achievement and cognitive ability?

Background

For more than twenty years, large and generally stable differences in academic achievement and cognitive ability have been reported within Germany. In such studies, the southern regions lead in the west and east, while city-states lag behind. Expressed in school learning time, the students in Bavaria are 14 months ahead of the students in Bremen. It is striking that there are no or only marginally received studies on causes and consequences.

Purpose

This study attempts to explore the causes and consequences of the differences within Germany and what can be learned in general about their development.

Materials and methods

We use data from student assessment and other studies (e.g., PISA, IQB) and apply correlational and path analyses, controlled for various background factors.

Results

There are no stable correlations with evolution (genes), educational level of society (adult school years) and wealth (GDP per capita). However, there are high correlations, robust across indicators, with "burgher-conservative" education policies, e.g., central exit examinations, early tracking, grades at a young age (around r ≈ .65); with measures of students' quantity of education (hours of instruction, no teacher shortage; r ≈ .40); with measures of tertiary educational quality and appreciation of education (university quality, short duration of studies, professors' salaries; r ≈ .50); with student native/immigrant ratio (r ≈ .50); with middle-class burgher lifestyle (less private debt, less welfare dependency and less crime; r ≈ .60); and with burgher-conservative-right politics (share of votes for CDU/CSU and non-left parties, non-left state governments; r ≈ .80). Longitudinal analyses over four decades reveal interaction effects, i.e., more burgher policies statistically lead to more cognitively competent students (β ≈ .45) and more cognitively competent populations vote for burgher parties (β ≈ .30).

Conclusions

The results, which support the efficacy a bourgeois-conservative education policy and of lower immigration rates, are delicate for the practice of student achievement research and for the political milieu that dominates the social sciences.

Half a century later and we're back where we started: How the problem of locality turned in to the problem of portability

In the 1970s, Lewontin sparked a debate about a problem of locality, by making the case that any given heritability estimate is local to the original population and environment studied, and could not be generalized to other populations and environments. Nearly 50 years later, a new problem of portability has emerged: the predictive accuracy of polygenic scores diminishes when applied to populations whose characteristics are different from the original population sample. This paper briefly reviews the nature of each problem and analyzes their similarities and differences in three areas: 1) conceptual underpinnings, 2) causal explanations, and 3) practical, social, and political implications. Although conceptually and methodologically different from the problem of locality in important respects, the problem of portability facing contemporary genomics today should come as no surprise, as it is an inevitable outcome of the kinds of problematic inferences detailed by Lewontin nearly half a century ago.

Between-Group Mean Differences in Intelligence in the United States Are >0% Genetically Caused: Five Converging Lines of Evidence

The past 30 years of research in intelligence has produced a wealth of knowledge about the causes and consequences of differences in intelligence between individuals, and today mainstream opinion is that individual differences in intelligence are caused by both genetic and environmental influences. Much more contentious is the discussion over the cause of mean intelligence differences between racial or ethnic groups. In contrast to the general consensus that interindividual differences are both genetic and environmental in origin, some claim that mean intelligence differences between racial groups are completely environmental in origin, whereas others postulate a mix of genetic and environmental causes. In this article I discuss 5 lines of research that provide evidence that mean differences in intelligence between racial and ethnic groups are partially genetic. These lines of evidence are findings in support of Spearman’s hypothesis, consistent results from tests of measurement invariance across American racial groups, the mathematical relationship that exists for between-group and within-group sources of heritability, genomic data derived from genome-wide association studies of intelligence and polygenic scores applied to diverse samples, and admixture studies. I also discuss future potential lines of evidence regarding the causes of average group differences across racial groups. However, the data are not fully conclusive, and the exact degree to which genes influence intergroup mean differences in intelligence is not known. This discussion applies only to native English speakers born in the United States and not necessarily to any other human populations.

How White nationalists mobilize genetics: From genetic ancestry and human biodiversity to counterscience and metapolitics

OBJECTIVES

Our aim in this study was to understand how genetics ideas are appropriated and mobilized online toward the political projects of White nationalism and the alt right. Studying three different online venues, we investigated how genetics is used to support racial realism, hereditarianism, and racial hierarchy. We analyzed how these ideas are connected to political and metapolitical projects. In addition, we examined the strategies used to build authority for these interpretations.

METHODS

We analyze three online venues in which genetics has been mobilized to advance racial realism and hereditarian explanations of racial differences. These were (a) the use of genetic ancestry tests in online nationalist discussions, (b) blogs and other venues in which the human biodiversity ideas are articulated, (c) activities surrounding the OpenPsych collection of online journals. Ethnographic and interpretive methods were applied to investigate scientific and political meanings of efforts to mobilize genetic ideas.

RESULTS

We found that White nationalists use genetic ancestry tests to align White identity with ideas of racial purity and diversity, educating each other about genetics, and debating the boundaries of Whiteness. "Human biodiversity" has been mobilized as a movement to catalog and create hereditarian ideas about racial differences and to distribute them as "red pills" to transform online discourse. The OpenPsych journals have allowed amateur hereditarian psychologists to publish papers, coordinate activity, and legitimate their project at the academic margins.

CONCLUSIONS

These various appropriations of genetics aim to further racial realism and hereditarian explanations of racial social and behavioral differences. Beyond these substantive aims, on a "metapolitical" level, they serve to reframe concepts and standards for political and scientific discussion of race, challenge structures of academic legitimacy and expertise, and build a cadre of ideological foot soldiers armed with an argumentative toolkit. As professional anthropologists and geneticists aim to accurately communicate their science and its implications for understanding human differences to the public, they must contend with these substantive claims and metapolitical contexts.

No support for the hereditarian hypothesis of the Black-White achievement gap using polygenic scores and tests for divergent selection

OBJECTIVES

Debate about the cause of IQ score gaps between Black and White populations has persisted within genetics, anthropology, and psychology. Recently, authors claimed polygenic scores provide evidence that a significant portion of differences in cognitive performance between Black and White populations are caused by genetic differences due to natural selection, the "hereditarian hypothesis." This study aims to show conceptual and methodological flaws of past studies supporting the hereditarian hypothesis.

MATERIALS AND METHODS

Polygenic scores for educational attainment were constructed for African and European samples of the 1000 Genomes Project. Evidence for selection was evaluated using an excess variance test. Education associated variants were further evaluated for signals of selection by testing for excess genetic differentiation (F_st ). Expected mean difference in IQ for populations was calculated under a neutral evolutionary scenario and contrasted to hereditarian claims.

RESULTS

Tests for selection using polygenic scores failed to find evidence of natural selection when the less biased within-family GWAS effect sizes were used. Tests for selection using F_st values did not find evidence of natural selection. Expected mean difference in IQ was substantially smaller than postulated by hereditarians, even under unrealistic assumptions that overestimate genetic contribution.

CONCLUSION

Given these results, hereditarian claims are not supported in the least. Cognitive performance does not appear to have been under diversifying selection in Europeans and Africans. In the absence of diversifying selection, the best case estimate for genetic contributions to group differences in cognitive performance is substantially smaller than hereditarians claim and is consistent with genetic differences contributing little to the Black-White gap.

Heritability of human visual contour integration-an integrated genomic study

Contour integration, a key visual function to deal with occlusion and discontinuity in natural scenes, is essential to human survival. However, individuals are not equally well equipped with this ability. In particular, contour integration deficiencies are commonly detected in patients with mental disorders, especially schizophrenia. To understand the underlying sources of these individual differences, the current study investigated the genetic basis of contour integration in humans. A total of 2619 normal participants were tested on their ability to detect continuous contours embedded in a cluttered background. Quantitative genomic analysis was performed, involving heritability estimation based on single nucleotide polymorphisms (SNPs) and association testing at SNP, gene, and pathway levels. Heritability estimation showed that common SNPs contributed 49.5% (standard error of the mean = 15.6%) of overall phenotypic variation, indicating moderate heritability of contour integration. Two-stage genome-wide association analysis (GWAS) detected four SNPs reaching genome-wide significance in the discovery test (N = 1931) but not passing the replication test (N = 688). Gene-level analysis further revealed a significant genome-wide association of a microRNA-encoding gene MIR1178 in both the discovery and replication cohorts. Another gene poly(A)-binding protein nuclear 1 like, cytoplasmic (PABPN1L) showed suggestive significance in the discovery cohort (p < 1 × 10^-4) and was replicated in the replication cohort (p = 0.009). The pathway analysis did not detect any significant pathway. Taken together, this study identified significant gene associations with contour integration and provided support for a genetic transmission of the ability to perceive continuous contours in the environment.

Race as Social Construct

It is often claimed that race is a social construct and that scientists studying race differences are disruptive racists. The recent April 2018 “Race Issue” of the widely distributed National Geographic Magazine (NG) provided its millions of readers with a particularly illustrative example of this position. As discussions of race issues often recur, in both scientific and lay literature, stir considerable polemics, and have political, societal and human implications, we found it of both scientific and general interest to identify and dissect the following partly overlapping key contentions of the NG race issue magazine: (1) Samuel Morton’s studies of brain size is reprehensible racism (2) Race does not relate to geographic location, (3) Races do not exist as we are all equals and Africans, (4) Admixture and displacement erase race differences as soon as they appear, and (5) Race is only skin color deep. Also examined is the claim that Race does not matter. When analyzed within syllogistic formalism, each of the claims is found theoretically and empirically unsustainable, as Morton’s continuously evolving race position is misrepresented, race relates significantly to geography, we are far from equals, races have definitely not been erased, and race, whether self-reported or defined by ancestry, lineage, ecotype, species, or genes, is much more than skin color deep. Race matters vitally for people and societies. We conclude that important research on existing population differences is hurt when widely respected institutions such as NG mobilize their full authority in a massively circulated attempt to betray its scientific and public readership by systematically misrepresenting historical sources and scientific positions, shaming past scientists, and by selectively suppressing unwanted or unacceptable results–acts included as examples of academic fraud by the National Academy of Sciences (US, 1986). Any unqualified a priori denial of the formative evolutionary aspects of individual and population differences threatens to impede the recent promising research on effects of genome wide allelic associations, which would lames us in the vital quest to develop rational solutions to associated globally pressing societal problems.

Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data

Genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment (EA) were used to test a polygenic selection model. Weighted and unweighted polygenic scores (PGS) were calculated and compared across populations using data from the 1000 Genomes (n = 26), HGDP-CEPH (n = 52) and gnomAD (n = 8) datasets. The PGS from the largest EA GWAS was highly correlated to two previously published PGSs (r = 0.96–0.97, N = 26). These factors are both highly predictive of average population IQ (r = 0.9, N = 23) and Learning index (r = 0.8, N = 22) and are robust to tests of spatial autocorrelation. Monte Carlo simulations yielded highly significant p values. In the gnomAD samples, the correlation between PGS and IQ was almost perfect (r = 0.98, N = 8), and ANOVA showed significant population differences in allele frequencies with positive effect. Socioeconomic variables slightly improved the prediction accuracy of the model (from 78–80% to 85–89%), but the PGS explained twice as much of the variance in IQ compared to socioeconomic variables. In both 1000 Genomes and gnomAD, there was a weak trend for lower GWAS significance SNPs to be less predictive of population IQ. Additionally, a subset of SNPs were found in the HGDP-CEPH sample (N = 127). The analysis of this sample yielded a positive correlation with latitude and a low negative correlation with distance from East Africa. This study provides robust results after accounting for spatial autocorrelation with Fst distances and random noise via an empirical Monte Carlo simulation using null SNPs.

Biogeographic Ancestry, Cognitive Ability and Socioeconomic Outcomes

The cause(s) of ubiquitous cognitive differences between American self-identified racial/ethnic groups (SIREs) is uncertain. Evolutionary-genetic models posit that ancestral genetic selection pressures are the ultimate source of these differences. Conversely, sociological models posit that these differences result from racial discrimination. To examine predictions based on these models, we conducted a global admixture analysis using data from the Pediatric Imaging, Neurocognition, and Genetics Study (PING; N = 1,369 American children). Specifically, we employed a standard methodology of genetic epidemiology to determine whether genetic ancestry significantly predicts cognitive ability, independent of SIRE. In regression models using four different codings for SIRE as a covariate, we found incremental relationships between genetic ancestry and both general cognitive ability and parental socioeconomic status (SES). The relationships between global ancestry and cognitive ability were partially attenuated when parental SES was added as a predictor and when cognitive ability was the outcome. Moreover, these associations generally held when subgroups were analyzed separately. Our results are congruent with evolutionary-genetic models of group differences and with certain environmental models that mimic the predictions of evolutionary-genetic ones. Implications for research on race/ethnic differences in the Americas are discussed, as are methods for further exploring the matter.

Biogeographic Ancestry, Cognitive Ability and Socioeconomic Outcomes

The cause(s) of ubiquitous cognitive differences between American self-identified racial/ethnic groups (SIREs) is uncertain. Evolutionary-genetic models posit that ancestral genetic selection pressures are the ultimate source of these differences. Conversely, sociological models posit that these differences result from racial discrimination. To examine predictions based on these models, we conducted a global admixture analysis using data from the Pediatric Imaging, Neurocognition, and Genetics Study (PING; N = 1,369 American children). Specifically, we employed a standard methodology of genetic epidemiology to determine whether genetic ancestry significantly predicts cognitive ability, independent of SIRE. In regression models using four different codings for SIRE as a covariate, we found incremental relationships between genetic ancestry and both general cognitive ability and parental socioeconomic status (SES). The relationships between global ancestry and cognitive ability were partially attenuated when parental SES was added as a predictor and when cognitive ability was the outcome. Moreover, these associations generally held when subgroups were analyzed separately. Our results are congruent with evolutionary-genetic models of group differences and with certain environmental models that mimic the predictions of evolutionary-genetic ones. Implications for research on race/ethnic differences in the Americas are discussed, as are methods for further exploring the matter.

Thought leader perspectives on benefits and harms in precision medicine research

Precision medicine research is underway to identify targeted approaches to improving health and preventing disease. However, such endeavors raise significant privacy and confidentiality concerns. The objective of this study was to elucidate the potential benefits and harms associated with precision medicine research through in-depth interviews with a diverse group of thought leaders, including primarily U.S.-based experts and scholars in the areas of ethics, genome research, health law, historically-disadvantaged populations, informatics, and participant-centric perspectives, as well as government officials and human subjects protections leaders. The results suggest the prospect of an array of individual and societal benefits, as well as physical, dignitary, group, economic, psychological, and legal harms. Relative to the way risks and harms are commonly described in consent forms for precision medicine research, the thought leaders we interviewed arguably emphasized a somewhat different set of issues. The return of individual research results, harm to socially-identifiable groups, the value-dependent nature of many benefits and harms, and the risks to the research enterprise itself emerged as important cross-cutting themes. Our findings highlight specific challenges that warrant concentrated care during the design, conduct, dissemination, and translation of precision medicine research and in the development of consent materials and processes.

Informed Consent in Translational Genomics: Insufficient Without Trustworthy Governance

Neither the range of potential results from genomic research that might be returned to participants nor future uses of stored data and biospecimens can be fully predicted at the outset of a study. Informed consent procedures require clear explanations about how and by whom decisions are made and what principles and criteria apply. To ensure trustworthy research governance, there is also a need for empirical studies incorporating public input to evaluate and strengthen these processes.

Cultural evolutionary theory: How culture evolves and why it matters

Human cultural traits-behaviors, ideas, and technologies that can be learned from other individuals-can exhibit complex patterns of transmission and evolution, and researchers have developed theoretical models, both verbal and mathematical, to facilitate our understanding of these patterns. Many of the first quantitative models of cultural evolution were modified from existing concepts in theoretical population genetics because cultural evolution has many parallels with, as well as clear differences from, genetic evolution. Furthermore, cultural and genetic evolution can interact with one another and influence both transmission and selection. This interaction requires theoretical treatments of gene-culture coevolution and dual inheritance, in addition to purely cultural evolution. In addition, cultural evolutionary theory is a natural component of studies in demography, human ecology, and many other disciplines. Here, we review the core concepts in cultural evolutionary theory as they pertain to the extension of biology through culture, focusing on cultural evolutionary applications in population genetics, ecology, and demography. For each of these disciplines, we review the theoretical literature and highlight relevant empirical studies. We also discuss the societal implications of the study of cultural evolution and of the interactions of humans with one another and with their environment.

Holocene Selection for Variants Associated With General Cognitive Ability: Comparing Ancient and Modern Genomes

Human populations living during the Holocene underwent considerable microevolutionary change. It has been theorized that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favored via directional selection genetic variants associated with higher general cognitive ability (GCA). To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4.56 to 1.21 kyr BP) with a sample of 503 modern European genomes (Fst= 0.013), using three different cognitive polygenic scores (130 SNP, 9 SNP and 11 SNP). Significant differences favoring the modern genomes were found for all three polygenic scores (odds ratios = 0.92,p= 001; .81,p= 037; and .81,p= .02 respectively). These polygenic scores also outperformed the majority of scores assembled from random SNPs generated via a Monte Carlo model (between 76.4% and 84.6%). Furthermore, an indication of increasing positive allele count over 3.25 kyr was found using a subsample of 66 ancient genomes (r= 0.22,pone-tailed= .04). These observations are consistent with the expectation that GCA rose during the Holocene.

SPEARMAN'S HYPOTHESIS TESTED COMPARING SAUDI ARABIAN CHILDREN AND ADOLESCENTS WITH VARIOUS OTHER GROUPS OF CHILDREN AND ADOLESCENTS ON THE ITEMS OF THE STANDARD PROGRESSIVE MATRICES

Spearman's hypothesis tested at the level of items states that differences between ethnic groups on the items of an IQ test are a function of the g loadings of these items, such that there are small differences between ethnic groups on items with low g loadings and large differences between ethnic groups on items with high g loadings; this has been confirmed in a limited number of studies. In this paper, Spearman's hypothesis was tested, comparing a group of Saudi children and adolescents (N=3209) with other groups of children and adolescents from Denmark, Cyprus, Croatia, Bosnia, South Africa, Estonia, Ukraine, Ireland, Russia and Chile (total N=9333). The analyses were carried out on twelve comparisons between the Saudi Arabian children and the other children. Spearman's hypothesis was confirmed less strongly than in other large-scale studies with a mean weighted r value of 0.44. The relevance of these findings for the discussion on the causes of group differences is discussed.

Cognitive Capitalism: Economic Freedom Moderates the Effects of Intellectual and Average Classes on Economic Productivity

Cognitive ability stimulates economic productivity. However, the effects of cognitive ability may be stronger in free and open economies, where competition rewards merit and achievement. To test this hypothesis, ability levels of intellectual classes (top 5%) and average classes (country averages) were estimated using international student assessments (Programme for International Student Assessment; Trends in International Mathematics and Science Study; and Progress in International Reading Literacy Study) (N = 99 countries). The ability levels were correlated with indicators of economic freedom (Fraser Institute), scientific achievement (patent rates), innovation (Global Innovation Index), competitiveness (Global Competitiveness Index), and wealth (gross domestic product). Ability levels of intellectual and average classes strongly predicted all economic criteria. In addition, economic freedom moderated the effects of cognitive ability (for both classes), with stronger effects at higher levels of freedom. Effects were particularly robust for scientific achievements when the full range of freedom was analyzed. The results support cognitive capitalism theory: cognitive ability stimulates economic productivity, and its effects are enhanced by economic freedom.