Archived analysis code for: Benning, John W., Jedidiah Carlson, Olivia S. Smith, Ruth G. Shaw, and Arbel Harpak. "Confounding Fuels Misinterpretation in Human Genetics." Proceedings of the Royal Society B (2025).

Abstract: The scientific literature has seen a resurgence of interest in genetic influences on human behavior and socioeconomic outcomes. Such studies face the central difficulty of distinguishing possible causal influences, in particular genetic and non-genetic ones. When confounding between possible influences is not rigorously addressed, it invites over- and misinterpretation of data. We illustrate the breadth of this problem through a discussion of the literature and a reanalysis of two examples. Clark (2023) suggested that patterns of similarity in social status between relatives indicate that social status is largely determined by one’s DNA. We show that the paper’s conclusions are based on the conflation of genetic and non-genetic transmission (for example, of wealth) within families. Song & Zhang (2024) posited that genetic variants underlying bisexual behavior are maintained in the population because they also affect risk-taking behavior and thereby confer an evolutionary fitness advantage through increased sexual promiscuity. In this case, too, we show that possible explanations cannot be distinguished, but only one is chosen and presented as a conclusion. We discuss how issues of confounding apply more broadly to studies that claim to establish genetic underpinnings to human behavior and societal outcomes.

This repository preserves the R workflows that accompany our article. The documents Clark2023.Rmd and SZ2024.R will reproduce the statistical analyses and figures reported in the paper. These repository files are licensed under CC BY.

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Note   No raw data are committed to GitHub because they are covered by the original authors’ CC BY license. Follow the steps in the next section to obtain them.

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Workflow

Data can be downloaded from the archived data sets accompanying Clark 2023 and Song and Zhang 2024 (see below). Analyses based on data from Clark 2023 data are done in R using Clark2023.rmd and analyses based on data from Song and Zhang 2024 data are done in R using SZ2024.R.

Data sources

Clark 2023 analyses

clark_reportedCors.csv contains the reported correlations in Clark (2023) Table 2 and is found in this repository.

All other data come from the supplementary datasets accompanying:

Clark, Gregory. "The inheritance of social status: England, 1600 to 2022." Proceedings of the National Academy of Sciences 120, no. 27 (2023): e2300926120.

Supplementary data can be found at https://www.pnas.org/doi/10.1073/pnas.2300926120#supplementary-materials. These datasets are licensed as CC-BY.

The supplementary data contain four Excel workbooks (Datasets 1–4) from which we extracted the following .csv files:

csv file	Source in Clark 2023 Supplementary data	Contents
clark_wealth.csv	Dataset 4, Figure 3 - ded occ lwealth tab	Maternal / paternal wealth and status
clark_lit.csv	Dataset 4, Figure 3 - Literacy tab	Literacy data
clark_fatherSon.csv	Dataset 4, Figure 4 tab	Father-son data, with son age at father death
clark_inds.csv	Dataset 1	Individual-level data
clark_rels.csv	Dataset 2, Table 2 1910‑97	Relative pair data for modern status measures
clark_rels_occ.csv	Dataset 2, Table 2 Occ Stat 1780-1919	Occupational status data
clark_rels_ded.csv	Dataset 3, Table 2 Ded 1780-1919	Higher education data
clark_rels_lit.csv	Dataset 3, Table 2 Literacy 1754-1889	Literacy data

Variable dictionary

This table lists the variables referenced in Clark2023.Rmd and used from the Clark (2023) supplementary datasets (Datasets 1–4), along with descriptions and units/scales as they are used in the analysis. See Clark (2023) for more details on construction of variables.

Variable	Description	Units / Scale	Notes
pid	Person identifier	ID (integer)
pidf, pidm, pidc	Person IDs for father (f), mother (m), child (c)	ID
pid_grandchild	Person ID for grandchild	ID
pidpgf, pidmgf	Person IDs for paternal / maternal grandfather	ID
relationship, relationship_rename	Kinship relation between two records	Categorical	Harmonized across datasets, where relationship names were not standardized
byr0, byr1	Birth year of pair member 0 / 1	Year (AD)
nid	Numeric lineage identifier	ID (integer)
lwealth	Log wealth	Unitless	Mean-centered log of estimated wealth
lwealthgc, lwealthpgf, lwealthmgf	Log wealth of grandchild / paternal GF / maternal GF	Unitless
occ	Occupational status score	Unitless index	Status scale as defined by Clark (2023)
occ0, occ1	Occupational status of pair member 0 / 1	Unitless index
occgc, occpgf, occmgf	Occupational status of grandchild / paternal GF / maternal GF	Unitless index
ded	Higher-education attainment indicator	Binary (0/1)	1 = degree/higher education
ded0, ded1	Higher-education indicator for pair member 0 / 1	Binary (0/1)
dedgc, dedpgf, dedmgf	Higher-education indicator (grandchild / paternal GF / maternal GF)	Binary (0/1)
lit	Literacy indicator	Binary (0/1)	1 = literate
lit0, lit1	Literacy indicator for pair member 0 / 1	Binary (0/1)
litf, litm, litc	Literacy of father / mother / child	Binary (0/1)
agedeathf	Individual's age at father's death	Years
imd	Index of multiple deprivation	Index	Weighted average of measures of social deprivation
lhv	log(house value)	Unitless	Natural log of house value
codir	Company director indicator	Binary (0/1)	Indicator of whether individual held a company directorship
statmod	Modern status	Index	PCA index of lhv, imd, and codir

Song and Zhang 2024 analyses

The file SZ2024.R contains code for our reanalysis of

Song, S., and J. Zhang. 2024. Genetic variants underlying human bisexual behavior are reproductively advantageous. Sci. Adv. 10:eadj6958.

Datasets containing GWAS summary statistics used in this analysis are available via Zenodo at https://doi.org/10.5281/zenodo.16994853.

Variable dictionary

This table lists the measures analyzed in SZ2024.R, which were derived from phenotype information in the UK Biobank. See Song and Zhang (2024) for more details on construction of the sexual behavior variables.

Measure	Description	Type	Notes
NC	Number of children	Quantitative
afs10	First had sex before age 10	Binary
afs13	First had sex before age 13	Binary
bsb	"bisexual behavior" as defined in Song & Zhang 2024	Binary
essb	"exclusively same-sex sexual behavior" as defined in Song & Zhang 2024	Binary
Ever_smoked		Binary
Ever_taken_cannabis		Binary
Maternal_smoking_around_birth		Binary
osb_any	"engaged in any opposite-sex sexual behavior" as defined in Song & Zhang 2024	Binary
Physically_abused_by_family_as_a_child		Binary
Recent_poor_appetite_or_overeating		Binary
risk_taking		Binary
ssb	"any same-sex sexual behavior" as defined in Song & Zhang 2024	Binary
Victim_of_sexual_assault		Binary
Age_first_had_sexual_intercourse		Quantitative
Average_total_household_income_before_tax		Quantitative
Falls_in_the_last_year		Quantitative
Frequency_of_solariumsunlamp_use		Quantitative
Length_of_working_week_for_main_job		Quantitative
Lifetime_number_of_sexual_partners		Quantitative
Loud_music_exposure_frequency		Quantitative
Number_of_full_brothers		Quantitative
Number_of_full_sisters		Quantitative
Weekly_usage_of_mobile_phone_in_last_3_months		Quantitative

Citing this code

If you build upon these scripts, please cite both our paper and the appropriate paper for the underlying data:

Benning, John W., Jedidiah Carlson, Olivia S. Smith, Ruth G. Shaw, and Arbel Harpak. "Confounding Fuels Misinterpretation in Human Genetics." Proceedings of the Royal Society B (2025).

Clark, Gregory. "The inheritance of social status: England, 1600 to 2022." Proceedings of the National Academy of Sciences 120, no. 27 (2023): e2300926120.

Song, S., and J. Zhang. 2024. Genetic variants underlying human bisexual behavior are reproductively advantageous. Sci. Adv. 10:eadj6958.

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Session and package info

 setting  value
 version  R version 4.5.1 (2025-06-13)
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 language (EN)
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 date     2025-09-04
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Contact

Please email [email protected].