The Proxy Problem Survives Even the Hardest Data

Ancient DNA has transformed our understanding of population history, but its potential to reveal as much about human evolutionary biology has not been realized because of limited sample sizes and the difficulty of distinguishing sustained rises in allele frequency increasing fitness—directional selection—from shifts due to migrations, population structure, or non-adaptive purifying or stabilizing selection. Here we present a method for detecting directional selection in ancient DNA time-series data that tests for consistent trends in allele frequency change over time, and apply it to 15,836 West Eurasians (10,016 with new data). Previous work has shown that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution8,9. By contrast, in the past ten millennia, we find that many hundreds of alleles have been affected by strong directional selection. We also document one-standard-deviation changes on the scale of modern variation in combinations of alleles that today predict complex traits. This includes decreases in predicted body fat and schizophrenia, and increases in measures of cognitive performance. These effects were measured in industrialized societies, and it remains unclear how these relate to phenotypes that were adaptive in the past. We estimate selection coefficients at 9.7 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.

When so many studies fail to be replicated, or draw different conclusions from the same set of facts, it does not instill confidence in the social sciences. Whether this is because of sloppy methodology, ideological infection, or other problems, the result is that even if there are right and wrong answers to many of our questions about human action, most social scientists are not yet in a position to find them. It is not that none of the work in social science is rigorous enough, but when policymakers (and sometimes even other researchers) are not sure which results are reliable, it drives down the status of the entire field. If medicine could break with its barbarous past, isn’t the same path open to the social sciences? For years, many have argued that if they could emulate the “scientific method” of the natural sciences, they too could become more scientific. But this simple advice faces several problems. Among the issues that plague contemporary social scientific research: Too much theory: A number of social scientific studies propose answers that have not been tested against evidence. The classic example here is neoclassical economics, where a number of simplifying assumptions — perfect rationality, perfect information — resulted in beautiful quantitative models that had little to do with actual human behavior. Lack of experimentation/data: Except for social psychology and the newly emerging field of behavioral economics, much of social science still does not rely on experimentation, even where it is possible. For example, it is sometimes offered as justification for putting sex offenders on a public database that doing so reduces the recidivism rate. This must be measured, though, against what the recidivism rate would have been absent the Sex Offender Registry Board (SORB), which is difficult to measure and has produced varying answers. This exacerbates the difficulty in (1), whereby favored theoretical explanations are accepted even when they have not been tested against any experimental evidence. Fuzzy concepts: Some social scientific studies can lead to misleading conclusions because of the use of “proxy” concepts for what one really wishes to measure. A recent example includes measuring “warmth” as a proxy for “trustworthiness,” in which researchers assumed — on the basis of studies which show that we are more likely to trust someone whom we perceive to be “on our side” — that perceptions of scientists as “cold” meant that they would be less trustworthy as well. But the two concepts may not be interchangeable. Ideological infection: This problem is rampant throughout the social sciences, especially on topics that are politically charged. Two ongoing examples are the bastardization of empirical work on the deterrence effect of capital punishment and the effectiveness of gun control on mitigating crime. If one knows in advance what one wants to find, one will likely find it. Cherry picking: The use of statistics allows multiple “degrees of freedom” to scientific researchers, but this is the most likely to be abused. In studies on immigration, for instance, a great deal of the difference between them is a result of alternative ways of counting the “costs” incurred by immigration. This is obviously also related to (4) above. If we know our conclusion, we may shop for the data to support it. Lack of data sharing: As the evolutionary biologist Robert Trivers reports in Psychology Today, there are numerous documented cases of researchers failing to share their data in psychological studies, despite a requirement from APA-sponsored journals to do so. When data were later analyzed, errors were found most commonly in the direction of the researcher’s hypothesis. Lack of replication: Psychology is undergoing a reproducibility crisis. One might validly argue that the initial finding that nearly two-thirds of psychology studies were irreproducible was overblown, but it is nonetheless shocking that most studies are not even attempted to be replicated. This can lead to difficulties, where errors can sneak through. Questionable causation: It is gospel in statistical research that “correlation does not equal causation,” yet some social scientific studies continue to highlight provocative results of questionable value. One recent sociological study, for instance, found that matriculating at a selective college was correlated with parental visitation at art museums, without explicitly suggesting that this was likely an artifact of parental income.