Sunday, October 21, 2018

The Truth Shall Make You Free

These NYTimes articles by Pulitzer Prize winner Amy Harmon, linking genetic science to racism and white supremacy, caused a sensation at ASHG 2018, a large annual meeting of genetics researchers.

Why White Supremacists Are Chugging Milk (and Why Geneticists Are Alarmed)

‘Could Somebody Please Debunk This?’: Writing About Science When Even the Scientists Are Nervous

Geneticists Criticize Use of Science by White Nationalists to Justify ‘Racial Purity’

In the second article above, Harmon writes

But another reason some scientists avoid engaging on this topic, I came to understand, was that they do not have definitive answers about whether there are average differences in biological traits across populations. And they have increasingly powerful tools to try to detect how natural selection may have acted differently on the genes that contribute to assorted traits in various populations.

What’s more, some believe substantial differences will be found. ...

One of the first talks I attended at ASHG this year is summarized below. The talk was oversubscribed, so I had to sit in the overflow room rather than the one with the speaker. One of the slides presented showed a table of specific complex traits, cross-referenced by different ancestry groups, indicating status of recent natural selection. The authors' results imply that different population groups have been experiencing differential selection over the last ~10k years: different selection pressures in different geographical locations. There were many talks at ASHG covering related topics, with similar conclusions. Advances in computational and statistical methods, together with large datasets, make it possible now to seriously investigate differential selection in recent human evolutionary history.

Given such results, how are researchers to respond when asked to categorically exclude the possibility of genetically mediated average differences between groups?

We are scientists, seeking truth. We are not slaves to ideological conformity.

Building genealogies for tens of thousands of individuals genome-wide identifies evidence of directional selection driving many complex human traits.

S.R. Myers 1,2; L. Speidel 1

1) Department of Statistics, University of Oxford, Oxford, United Kingdom; 2) Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom

For a variety of species, large-scale genetic variation datasets are now available. All observed genetic variation can be traced back to a genealogy, which records historical recombination and coalescence events and in principle captures all available information about evolutionary processes. However, the reconstruction of these genealogies has been impossible for modern-scale data, due to huge inherent computational challenges. As a consequence, existing methods usually scale to no more than tens of samples. We have developed a new, computationally efficient method for inferring genome-wide genealogies accounting for varying population sizes and recombination hotspots, robust to data errors, and applicable to thousands of samples genome-wide in many species. This method is >10,000 times faster than existing approaches, and more accurate than leading algorithms for a range of tasks including estimating mutational ages and inferring historical population sizes. Application to 2,478 present-day humans in the 1000 Genomes Project, and wild mice, provides dates for population size changes, merges, splits and introgressions, and identifies changes in underlying evolutionary mutation rates, from 1000 years, to more than 1 million years, ago. Using our mutational age estimates, we developed an approach quantifying evidence of natural selection at each SNP. We compared resulting p-values to existing GWAS study results, finding widespread enrichment (>2.5-fold in Europeans and East Asians) of GWAS hits among individual SNPs with low selection p-values (Z>6), stronger than the 1.5-fold increase observed at nonsynonymous mutations, and with enrichment increasing with statistical significance. We found evidence that directional selection, impacting many SNPs jointly, has shaped the evolution of >50 human traits over the past 1,000-50,000 years, sometimes in different directions among different groups. These include many blood-related traits including blood pressure, platelet volume, both red and white blood cell count and e.g. monocyte counts; educational attainment; age at menarche; and physical traits including skin colour, body mass index and (particularly in South Asian populations) height. Our approach enables simultaneous testing of recent selection, ancient natural selection, and changes in the strength of selection on a trait through time, and is applicable across a wide range of organisms.

Of course, all good people abhor racism. I believe that each person should be treated as an individual, independent of ancestry or ethnic background. (Hence I oppose Harvard's race-based discrimination against Asian Americans and favor Caltech's meritocratic approach to admissions.)

However, this ethical position is not predicated on the absence of average differences between groups. I believe that basic human rights and human dignity derive from our shared humanity, not from uniformity in ability or genetic makeup.

As a parent it is obvious to me that my children differ in innate aptitudes, preferences, and personalities. I love them equally: it would be wrong to condition this love on their specific genetic endowments.

Here is another set of ASHG talks I attended, on related issues:

Impact of Natural Selection on the Genetic Architecture of Complex Traits

Moderators: Shamil Sunyaev, Harvard Med Sch & Brigham & Women’s Hosp, Boston

Laura Hayward, Columbia Univ, New York

Evolution and maintenance of complex traits under natural selection has been a long-standing area of genetic research. Polygenic adaptation, stabilizing selection, and negative selection on new mutations can substantially impact the genetic architecture of diseases and complex traits, via direct selection on traits that are correlated with fitness and/or via pleiotropic selection. New methods are being developed to detect the action of natural selection at different time scales, including selection in contemporary humans. This session will discuss recent work on methods that analyze data from large cohorts to detect natural selection and evaluate its impact on diseases and complex traits. The application of these methods has substantially improved our understanding of polygenic disease and complex trait architectures, informing efforts to identify and interpret genetic variation affecting diseases and complex traits.

10:30 AM Polygenic architecture and adaptation of human complex traits. J. Pritchard. Howard Hughes Med Inst, Stanford.

11:00 AM Detection and quantification of the effect of selection and adaptation on complex traits. P. Visscher. Univ Queensland, Brisbane, Australia.

11:30 AM Observing natural selection in contemporary humans. M. Ilardo. Univ Utah & UC Berkeley.

12:00 PM Impact of negative selection on common variant disease architectures. A. Price. Harvard TH Chan Sch Publ Hlth, Boston.

More papers on recent natural selection and human complex traits:

https://infoproc.blogspot.com/2015/10/genetic-group-differences-in-height.html

https://infoproc.blogspot.com/2016/05/evidence-for-very-recent-natural.html

https://infoproc.blogspot.com/2017/06/complex-trait-adaptation-and-branching.html

https://infoproc.blogspot.com/2017/07/natural-selection-and-body-shape-in.html

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37072883)

I know XOXO will react in horror to the "all good people abhor racism" part, but this really needs to be forcememed to the masses. It shouldn't even be controversial.

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073170)

stephen hsu is a very smart guy

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073225)

Based on what Hsu has actually written, I think he and I have the same perspective: There is near irrefutable evidence for on-average differences between groups, and there is also strong evidence that these differences are not just the result of cultural conditioning. Nonetheless, that does not justify treating an individual differently simply based on the average tendencies of a group that the individual belongs to.

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073321)

and good luck tricking other people of this same thing

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073571)

i guess that is "nutty" for me and you and everyone else alive today, since you and i and everyone else alive today have never known anything else in our lives. but really not nutty or unreasonable or crazy at all when you think about how humans have always lived

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073652)

it is, in fact, justified. it is something that we all do every day, all the time. you're never going to convince a thinking person that there's anything wrong with this

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073965)

The reason I don't believe it is justified in most cases is that there is more directly relevant information to whatever characteristic you are trying to judge that can be obtained in mere seconds in almost all situations. If you speak to someone for thirty seconds, you can probably get a better feel for many of their characteristics than simply having the knowledge that they are a black male Christian. That doesn't mean you need to *ignore* things you know to be unusually common among black male Christians.

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37074011)

definitely a serious, well thought out position by someone who actually grasps this subject matter and is not just repeating vague feel-good inaccurate aphorisms that he has picked up from the lib machine over time

if it makes you feel any better, this is the standard incoherent regurgitation of this talking point that i've gotten from every single lib, ever, in my entire life. so you're in good (?) company

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37074194)

Let's start simple. Can you agree that there is a wide middle ground between ignoring information and make a decision/taking an action based solely on that information?

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37074212)

More broadly (not aimed at you)- And why is it taken for granted that widespread acceptance / acknowledgement of this topic leads to worse outcomes for the disadvantaged groups, rather than better outcomes due to both sides finally being able to understand and agree rather than forced to lies?

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073939)

Are you new to xoxo? This place is Exhibit A for people's tendency to lump people in with their most easily-identifiable demographic group.

As for your second question, because people are by and large morons.

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073964)

For what it's worth, you're doing a good job convincing me that the pattern recognition device in your head is not actually very "finely tuned."

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073924)

Anything like genetic IQ differences is a direct threat to one of their core beliefs and therefore must be eradicated.

When you see Liberalism as a religion, all can be explained.

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073653)

Which is racist on the ground that it fails to brand all whites as oppressors.

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37073804)

https://www.reddit.com/r/samharris/comments/9q7kdg/the_truth_shall_make_you_free_stephen_hsu_on/

sillywabbit45

"So, I looked up Stephen Hsu. He's a physicist who's now in university administration at MSU. He's a legit academic heavyweight, very impressive guy. Still, it appears he doesn't actually do any research on this topic, or anything remotely related to genetics.

​

I guess it's fine to speculate about different selection pressures among "populations". The core weakness of bio-determinist claims about race and intelligence that I see is that current science doesn't seem to be able to identify clear groups of people that map onto our contemporary understanding of "race", nor have we effectively identified the genetic basis for intelligence. At this point, claims like Hsu's are speculative. Notice the lack of documentation in his blog post- if it weren't speculative he'd be citing dozens of academic articles. He seems to be implying a lot from a single article, which doesn't make the same implications he does.

​

When the whole Murray thing went down, I was frankly surprised by the sheer volume of people that believed that the science clearly showed that 1) "race" as defined in the contemporary US maps neatly onto clearly distinct, genetic groups of people and 2) the current science has shown that the causal mechanism behind racial differences in IQ are genetic differences between races. The research simply isn't there, though often I'll see people making these claims.

​

Also, we really need to drop this strawman that "the left" doesn't acknowledge group differences. I think the point is that some of us challenge sloppy bio-determinist claims that are made with no evidence. Also, a while back someone posted a neat article that asked people of various political stripes their views on the source of social inequality. Republicans, at least in the general public, were actually quite skeptical of genetic causation. I suspect that this may be rooted in some Republicans' belief in meritocracy, competition, personal responsibility, etc- all notions that are difficult to square with a strong genetic determinist position."

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37074289)

that is...neither how it appears nor is

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37074395)

This seems to be the new shitlib canned response. Why would it matter if genetic clusters matched our contemporary understanding of race whatever that means

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37074441)

but its false.

everyone gets the result from 23andme that they checked off before getting DNA testing. there is quite literally zero discrepancy.

(http://www.autoadmit.com/thread.php?thread_id=4112421&forum_id=2#37074519)