Journal club – eugenics and stuffMaximilian PressOctober 7, 2014 – UW Genome Sciences
Content note
• Eugenics
• Racism
• Bad science
What is eugenics?“…the science which deals with the influences that improve the inborn qualities of a race…and encourage action in the direction of perpetuating a higher racial standard.” Encyclopaedia Brittanica (1910)
What is eugenics?“…the science which deals with the influences that improve the inborn qualities of a race…and encourage action in the direction of perpetuating a higher racial standard.” Encyclopaedia Brittanica (1910)
“…a social philosophy advocating the improvement of human genetic traits…” Wikipedia (2014)
Early genetics ~= eugenics
wikipedia
• Francis Galton• Karl Pearson• Charles Darwin• Theodore Roosevelt• Margaret Sanger• Cold Spring Harbor
Laboratory• Alexander G. Bell• Rockefeller Foundation • Ronald A. Fisher
• Linus Pauling• John M. Keynes• Winston Churchill
International EugenicsCongress, 1921
Early genetics ~= eugenics
wikipedia
• Francis Galton• Karl Pearson• Charles Darwin• Theodore Roosevelt• Margaret Sanger• Cold Spring Harbor
Laboratory• Alexander G. Bell• Rockefeller Foundation • Ronald A. Fisher
• Linus Pauling• John M. Keynes• Winston Churchill
NOT Thomas H. Morgan
Eugenics penetrated into popular culture
Kansas exhibition 1929(?)
Eugenics had a racial, evolutionary focus
E. Haeckel (1903), Anthropogenie: oder, Entwickelungsgeschichte des Menschen
The Bell Curve: IQ and race
The Bell Curve: IQ and race
• Often taken to represent “intelligence” (controversial)
• Heritability: 40-80% (twin studies)
• Affected by socioeconomic/cultural factors
• Correlated with economic success
The Bell Curve: IQ and race
IQ is an “objective” measure that can be used to evaluate and rank people.
The Bell Curve: IQ and race
“…on the whole, America had already achieved enough objective equalization in its schools by 1964 so that it was hard to pick up any effects of unequal school quality.”
“It is sometimes suggested that the Black/White differential in psychometric intelligence is partly due to genetic differences (Jensen, 1972). There is not much direct evidence on this point, but what little there is fails to support the genetic hypothesis.”-American Psychological Association task force (1996)
“It is sometimes suggested that the Black/White differential in psychometric intelligence is partly due to genetic differences (Jensen, 1972). There is not much direct evidence on this point, but what little there is fails to support the genetic hypothesis.”-American Psychological Association task force (1996)
(3 variants explain ~3 IQ points)
Bell Curve spinoffs
• Nicholas Wade, A Troublesome Inheritance (2014)
Bell Curve spinoffs
• Nicholas Wade, A Troublesome Inheritance (2014)
• Richard Lynn, The Global Bell Curve (2008)– Many societies are racially diverse, not just USA– “consistent evidence of race-based social hierarchies”
(wikipedia)
The papers today
Author Year Journal Reviewed?D. Piffer 2013 Mankind Quarterly +D. Piffer 2014 IBC +/-D. Piffer 2014 BioRxiv -
The papers today
Author Year Journal Reviewed? dataD. Piffer 2013 Mankind Quarterly + 1KG, HapMapD. Piffer 2014 IBC +/- 1KGD. Piffer 2014 BioRxiv - 1KG
The papers today
Author Year Journal Reviewed? dataD. Piffer 2013 Mankind Quarterly + 1KG, HapMapD. Piffer 2014 IBC +/- 1KGD. Piffer 2014 BioRxiv - 1KG
The papers today
Author Year Journal Reviewed? dataD. Piffer 2013 Mankind Quarterly + 1KG, HapMapD. Piffer 2014 IBC +/- 1KGD. Piffer 2014 BioRxiv - 1KG
Reviewer 2: Richard Lynn, University of Ulster
Reviewer 2: Richard Lynn, University of Ulster
Reviewer 2: Richard Lynn, University of Ulster
Reviewer 2: Richard Lynn, University of Ulster“This is a highly innovative paper that presents novel statistical tools to detect recent polygenic selection, by using open access data sets available to everyone. I foresee fruitful developments based on the ideas presented in this paper and a cascade of publications centered on this neglected but extremely important topic.”
The papers today
Author Year Journal Reviewed? phenotypeD. Piffer 2013 Mankind Quarterly + IQD. Piffer 2014 IBC +/- heightD. Piffer 2014 BioRxiv - IQ
The papers today
Author Year Journal Reviewed? phenotypeD. Piffer 2013 Mankind Quarterly + IQD. Piffer 2014 IBC +/- heightD. Piffer 2014 BioRxiv - IQ
Polygenic selection
Polygenic selection
Pritchard et al. 2010
Polygenic selection
Variants under a polygenic selection should be:• Correlated with each other in their allelic distribution• Correlated with the phenotype in question
Pop rs1 rs2 rs3 rs4 rs5 rs6 rs7 rs8 … rsN
CEU
YRI
CHB
Data: 1000 genomes data for 89 SNPs associated with height (Lango Allen et al. 2009) average height measurements for 14 1000 genomes populations
GWAS SNPs
1KG
popu
latio
ns
Pop rs1 rs2 rs3 rs4 rs5 rs6 rs7 rs8 … rsN
CEU .32 …
YRI .49
CHB .25
Data: 1000 genomes data for 89 SNPs associated with height (Lango Allen et al. 2009) average height measurements for 14 1000 genomes populations
Divided into 9 bins, allele frequencies
GWAS SNP frequencies
1KG
popu
latio
ns
Pop rs1+2 rs3+4 rs5+6 rs7+8 rsN-1+N
CEU .32
YRI .49
CHB .25
Data: 1000 genomes data for 89 SNPs associated with height (Lango Allen et al. 2009) average height measurements for 14 1000 genomes populations
Divided into 9 bins, allele frequencies averaged within bins for each population
GWAS SNP average frequencies
1KG
popu
latio
ns
Data: 1000 genomes data for 89 SNPs associated with height (Lango Allen et al. 2009) average height measurements for 14 1000 genomes populations
Divided into 9 bins, allele frequencies averaged within bins for each population PCA on 14 x 9 matrix of meta-allele frequencies
Pop rs1+2 rs3+4 rs5+6 rs7+8 rsN-1+N
CEU .32
YRI .49
CHB .25
GWAS SNP average frequencies
1KG
popu
latio
ns
PCA for “factor” extractionSA
LARY
HOURS WORKED / WEEK
PCA for “factor” extractionSA
LARY
HOURS WORKED / WEEK
PCA for “factor” extractionSA
LARY
HOURS WORKED / WEEK
PC1: “CAPITALIST SCORE”
PC2: “LUCK”
PCA for “factor” extraction
Person Capitalism Luck
Lisa 10 -5
Frank 0 5
Erin 5 0
PC1: “CAPITALIST SCORE”
PC2: “LUCK”
PCA for “factor” extraction
PC1: “CAPITALIST SCORE”
PC2: “LUCK”
Person Capitalism Luck Happiness
Lisa 10 -5 3
Frank 0 5 -5
Erin 5 0 1
PCA for “factor” extraction
PC1: “CAPITALIST SCORE”
PC2: “LUCK”
Person Capitalism Luck Happiness
Lisa 10 -5 3
Frank 0 5 -5
Erin 5 0 1
Being a capitalist (PC1) makes you happier than being lucky (PC2).
PCA to get a “polygenic score”
Alle
le 2
freq
uenc
y
Allele 1 frequency
PC1
PC2
PCA to get a “polygenic score”
Alle
le 2
freq
uenc
y
Allele 1 frequency
Population PC1 PC2
CEU 10 7
YRI 0 5
CHB 5 0
PC1
PC2
Go fishing for a PC correlated to height
Alle
le 2
freq
uenc
y
Allele 1 frequency
Population PC1 PC2 height
CEU 10 7 180
YRI 0 5 178
CHB 5 0 170
PC1
PC2
Fishing for a ‘height’ factor
(imaginary)
Fishing for a ‘height’ factor
(provided in paper)
Fishing for a ‘height’ factor
r = 0.98 (? 0.84)P = 0.02 (? 6e-5)
Fishing for a ‘height’ factor
r = 0.98 (? 0.84)P = 0.02 (? 6e-5)
East Asian populations
Populations of EuropeanAnd African descent
The papers today
Author Year Journal Reviewed? phenotypeD. Piffer 2013 Mankind Quarterly + IQD. Piffer 2014 IBC +/- heightD. Piffer 2014 BioRxiv - IQ
Mankind Quarterly paper: same, but for IQ
Mankind Quarterly paper: same, but for IQ
Mankind Quarterly paper: same, but for IQ
r = 0.9P < 0.001
Mankind Quarterly paper: same, but for IQ
r = 0.9P < 0.001
East Asian populations
Populations of European descent
Populations of African descent
Admixed Latin American populations
Mankind Quarterly paper: same, but for IQ
r = 0.9P < 0.001
East Asian populations
Populations of European descent
Populations of African descent
Admixed Latin American populations
???
Explanation?
What do you see (PC1 and PC2) when you do PCA on 1KG data?
What do you see (PC1 and PC2) when you do PCA on 1KG data?
1000 Genomes, Nature (2012)
What do you see (PC1 and PC2) when you do PCA on 1KG data?
1000 Genomes, Nature (2012)
(African descent vs. everyone else)
(Eas
t Asia
n de
scen
t vs
. eve
ryon
e el
se)
What do you see (PC1 and PC2) when you do PCA on 1KG data?
1000 Genomes, Nature (2012) “IQ” PC1?
What do you see (PC1 and PC2) when you do PCA on 1KG data?
1000 Genomes, Nature (2012)
“Height” PC2?
So basically Piffer’s signal is all population structure?
So basically Piffer’s signal is all population structure?
• yes
So basically Piffer’s signal is all population structure?
• yes
This kind of thing only happens in weird, obscure journals, right?
This kind of thing only happens in weird, obscure journals, right?
• no
Bad genetics elsewhere
Ashraf and Galor, American Economic Review (2013)
Bad genetics elsewhere
Ashraf and Galor, American Economic Review (2013)
Bad genetics elsewhere
Ashraf and Galor, American Economic Review (2013)
Bad genetics elsewhere
Conclusions
• Eugenics is alive and well
Conclusions
• Eugenics is alive and well
• Ideologically motivated researchers:– read genetics literature– use openly available data– exploit modern research dissemination venues– act unethically to get papers published
Conclusions
• Eugenics is alive and well
• Ideologically motivated researchers:– read genetics literature– use openly available data– exploit modern research dissemination venues– act unethically to get papers published
• Mainstream researchers do weird things with genetic data too, they just get challenged on it
Some questions
• How do we feel about unethical researchers having access to data?
• Should genomicists do more to counter flawed analyses of genomic data?
• Is it worth paying attention to marginal research communication venues?
Some questions
• How do we feel about unethical researchers having access to data?
• Should genomicists do more to counter flawed analyses of genomic data?
• Is it worth paying attention to marginal research communication venues?
Some questions
• How do we feel about unethical researchers having access to data?
• Should genomicists do more to counter flawed analyses of genomic data?
• Is it worth paying attention to marginal research communication venues?
Acknowledgments
Sarah
Queitsch Lab
Questions or thoughts?
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