In Education Week, a black lady reporter ponders a perennial question with less bigotry and hate than is the norm these days:
Who’s to Blame for the Black-White Achievement Gap?
By Christina A. Samuels
January 7, 2020My SAT scores might have remained a bit of trivia had I not become an education reporter. But my career has given me a reason to think a lot about testing, and what seems to be an intractable test-score gap between black students (as well as Hispanic and American Indian and Alaska Native students) and white and Asian students.
It sounds naive, but at the start of my career as an education reporter, I really wondered: Why is there such a big black-white test gap? I mean, I’m no genius, but I did OK. Why does this gulf never seem to close?
It’s becoming easier to look at the SATs, specifically, and say those scores don’t matter any more. Some of the nation’s most exclusive colleges and universities—Bowdoin, Wake Forest, the University of Chicago, and other well-respected liberal arts institutions—have become test-optional. It’s an ironic dismissal of a test that was originally created to bring equity to the college admissions process.
But the same ethnic and racial gaps exist across all kinds of tests, not just assessments for college admissions. One could argue that the SAT is too easily influenced by outside factors, such as test-prep classes. But students don’t prep for the National Assessment for Educational Progress, and the so-called “Nation’s Report Card” shows similar gaps.
Good point.
Teachers have one of the closest views of student performance, and Education Week recently asked them what they believe are the factors that explain why white students, overall, perform better academically than black students. (The survey respondents were predominantly white, like the teaching population as a whole, with 20 to 30 years in the classroom.)
Due to education reforms in the 1990s to give students better teachers, the public school teaching profession at present has surprisingly little affirmative action (public school administration, in contrast, has a lot).
The teachers were given a number of factors to choose from: genetics, discrimination, school quality, student motivation, parenting, income levels, home environments, and neighborhood environments.
The explanation of student performance, those teachers said, rests primarily with the students and their parents. Three-quarters or more of respondents said that motivation, parenting, income, home environments, and neighborhood environments explained student academic gaps “somewhat,” “quite a lot,” or “extremely.”
Seventy-two percent said “school quality” was a major factor. A little less than half said that discrimination played a major role.
A notable minority, about 29 percent, said that genetics are somewhat to extremely significant in explaining academic gaps between black students and white students. (An even higher percentage of respondents, 38 percent, said genetics are a significant reason why Asian students in the aggregate have better academic outcomes than their white peers.)
I bet the ~25% of teachers who said yes on both the white-black and Asian-white gaps having a genetic component are likely to give better practical advice on how to improve schooling than are the True Believers. Of course, any study that searched out courageous realist teachers to find out their advice would likely turn into a Let a Hundred Flowers Bloom (and then chop them off) situation.
But “black” is as much a social construct as it is a matter of genetic heritage: I have two black parents and call myself black. So does Barack Obama, who has one white parent. So does Kamala Harris, a U.S. senator from California, who has one parent from India. The category of “black” is fluid, as are other racial and ethnic categories—and geneticists agree that we are more different from each other as individuals, than we are as populations grouped by “race.”
Okay, but that actually works in the opposite direction. A lot of people who use this argument don’t realize that the fact that self-identified blacks include lots of people with substantial white ancestry, some of them high scorers like Barack Obama, would tend to narrow the test score gap.
I was defensive and annoyed when I analyzed the results of this survey. “It’s not our fault!” seemed to be the takeaway from teachers, but kids spend up to 13 years of their lives in school. Of course what happens there is relevant.
But I have to acknowledge some truth in what these teachers are saying. Yes, it mattered that my parents were middle-class, college-educated folks who filled my childhood home with books.
She ends up focusing on wealth as an explanation, which doesn’t really do it. But I appreciate the general tone of the article, which is much more civil and sensible than is common in 2020.
Also I didn’t see the word “hair” anywhere in Ms. Samuels’ article. It’s like a Blast from the Past.


RSS


One thing this passage reveals is that the survey wasn’t anonymous, or at least it depends on self-reported qualities. Given the subject matter, both of these facts are likely significant.
And this is what we call “Science” in the year 2020.
All the alleged causative factors could be confirmed or ruled out by properly designed studies that held other factors constant.
But yet it never fails, the fallback answer is always to blame some mystery factor that can't be identified, but that also has some rough correlation to income. Gee, what could it be? We'll just have to keep funding more studies and surveys.
Is this really true for Caucasian and Asian students? Or is the de facto test drop only applicable to NAMs and to children of wealthy donors? Let’s hope that it’s the latter, or else the rot has spread beyond the soft bigotry of low expectations zone.
Come quickly, repeal of Griggs v. Duke Power!
The poor woman , she seems to be on the verge of noticing .
Could be the fault of the airlines, at least today in Los Angeles; what with their gassing of the students:
For some of the respondents, maybe this is a roundabout way of ascribing it to genetics of the students and their parents.
Yeah, it is pretty common that kids who grow up in stable, middle class, homes with two involved parents who encourage them to read and to do well in school tend to do better in school than the “ghetto” kids, as my kids call them. Whatever the race.
It appears to me that the vast majority of the factors which lead to the test score disparities take place outside the school. Many factors take place before the kid starts pre-school. Some factors take place before the kid is ever born. And we don’t know the exact percentages, and I doubt we will, at least not in the next century or so.
Of course, the school boards decide all the burden of fixing all these problems lies with the teachers.
“Teachers have one of the closest views of student performance, and Education Week recently asked them what they believe are the factors that explain why white students, overall, perform better academically than black students”
How come they never ask why Northeast Asians perform better then White students.
This woman is obviously an idiot.
Evidently they did. From the article.."(An even higher percentage of respondents, 38 percent, said genetics are a significant reason why Asian students in the aggregate have better academic outcomes than their white peers.)"
Education like the Postal Service is a Jobs Program for the Community. Once hired you can’t be fired.
Let’s see. Hmmmm.
Who are we to blame?
Answer: The same dastardly people who are responsible for the black-Asian achievement gap?!
Could it be?
Or maybe it’s those other sneaky villains… the ones who are responsible for the Hispanic-Asian achievement gap?!
No it can’t be.
Just who are the gap makers? And why should they remain free to run around making gaps?
People often point to the poor living conditions of blacks as part of the explanation of the black-White gap. And it definitely plays some role. But it also plays a role in White outcomes too. Whites have been upended for quite some time now. The number of White kids from divorced homes is at levels that people 50 years ago would not imagine. The social rot and drug use that has affected blacks has also had an effect on Whites.
So if you argue that the poor living conditions of blacks has contributed to the gap, then it has also contributed to the gap being narrower since many Whites are not producing up to their potential due to similar circumstances.
Though I have no problem accepting that NE Asians have higher IQs, would the Asian-White gap be as high as it is now if Whites had the better family structure of the NE Asians?
I don’t think that stands up to scrutiny–in New York State, at least. The State Education Department has been dumbing-down the state teacher certification exams–especially in response to poor minority (mostly black) passing rates, where another achievement “gap” proliferates.
God.
Darwin.
It’s like they refuse to see what’s right in front of them.

So, we should be satisfied that they don’t call hereditarians evil racists all the while they ignore the obvious hereditarian evidences.
Chechens? 😉
“Yes, it mattered that my parents” passed down through to me their genetic material. Better students start with better eggs, that’s the Headstart that that matters.
Who is to blame?
Round up the usual (white, male) suspects!
If I was to hazard a guess about the cause of the gap I might say while one set of kids was memorizing lyrics to the latest hip-hop recording, the other set was busy hitting the books.
But closing say half of it would be nice. But to do that you'd have to do social interventions far beyond what our society would tolerate. Turning a ghetto family into an Asian Tiger family is no small thing. Nothing you do at school is going to help because the kid is with his family 87% of the time.
I’d be interested to see what kind of gap would come out of the ASVAB, which the US military has been administering in one form or another for over a century, and probably has a data set in the tens of millions.
Particularly I’d be interested to know what the gap was for poor depression era whites and blacks from the rural South heading into WWII. This might take some of these post ’60s variables out of the equation.
Probably related to:
The SAT gap isn’t personal for her.
I'd be curious how she sees herself intelligence wise compared to other black people she interacts with. If there are many she is likely to be quite smart in those groups. Maybe she assume it's just because she's more learned and that's all that's going on?
(just speaking statistically)
Is there a gap for students of the same IQ regardless of race? Any studies been done on that?
God Almighty or evolution… take your pick.
Two pet peevey points:
1. “… geneticists agree that we are more different from each other as individuals, than we are as populations grouped by “race.”
This is true. What it means is that although the mean IQ of blacks and whites are a single standard deviation apart, if you look at all blacks, they are spread over four or six or more standard deviations, as are all whites, and these spans mostly overlap.
So for the most part, at any IQ level there are blacks and whites.
However, the 1 SD difference (as well as a narrower variance) means that there are substantially fewer blacks, proportionally to their representation in the population, than whites, at any IQ over about 80, and the higher you go, the more disproportionate things get (and at the extreme right tail blacks disappear altogether).
For instance, 25 percent of whites have IQs over 110 (the old fashioned de facto cutoff for university attendance and the professions), while less than 3 percent of blacks reach that level. Taking current United States race percentages, 62 percent non-Hispanic white and 13 percent black, and simplifying things by assuming that there are only blacks and non-Hispanic whites, a 1,000-member entering class at a university would contain about 980 n-H whites and 20 blacks, if admissions were based on random selection of all applicants reaching a minimum threshold of an IQ of 110, and it would be worse if admissions were done in rank order from the top down.
And yet, indeed, it is still true that “we are more different from each other as individuals, than we are as populations grouped by race.”
2. “Yes, it mattered that my parents were middle-class, college-educated folks who filled my childhood home with books.”
This will never die, I suppose, but the “book access” theory of IQ has long since been debunked (as has the MSG Chinese restaurant syndrome, but that also lives on in folklore), including by twin studies. Rather than her parents’ “filling her home with books,” her father “filled her mother’s vagina with semen,” which, after fertilization gave the writer a genome that created a person with sufficient intelligence to appreciate books and seek them out, just as her parents’ genomes motivated them to fill their home with books. If adopted by illiterates at birth, she still would have nagged someone into taking her to the library.
Short of the feral child raised by wolves situation, a smart kid will one way or another get ahold of books, whatever the home situation is, and a dumb kid will ignore books if they are not shoved down his throat, and if shoved down his throat, any effect will fade out within two years.
At this particular moment in our culture, a return to citing the home/neighborhood for poor black student performance (and everything else) would be a huge improvement over the current standard explanation of white supremacy, redlining, over discipline, etc. It’s only half an answer, but there is truth behind it.
How come they never ask why Northeast Asians perform better then White students.
This woman is obviously an idiot.
How come they never ask why Northeast Asians perform better then White students.
Evidently they did. From the article..“(An even higher percentage of respondents, 38 percent, said genetics are a significant reason why Asian students in the aggregate have better academic outcomes than their white peers.)”
FWIW, my otherwise almsot completely apolitical family member, who is the division chief of one of the most important divisions in a major US state (ostensibly conservative) med school, is reporting concern over med school student admissions choose students for PC reasons over academic performance. The normies are waking up.
“Also I didn’t see the word “hair” anywhere in Ms. Samuels’ article. ”
Yeah….but you know she was thinking about it.
Speaking of true believers…
I knew a teacher born in Minnesota in the 1920s, brought up in a traditional Lutheran environment, who taught for decades in an LA County suburb. Her experience with younger, idealistic teachers taught her that the most trustworthy metric for predicting whether such a person was going to swim or sink in her increasingly diversifying district was a firm belief in Original Sin.
Now that’s the ultimate genetic factor!
Not sure why you think Obama had high test scores. Despite multiple probings from Trump, Obama never released his SAT scores. There are rumors he scored even lower than George W. And his daughter Malia’s scores are lower still.
If you assume a high score is necessary to get into Columbia, well, he didn’t get into Columbia. He got into Occidental, then transferred to Columbia under the guaranteed transfer program for minorities. It’s the backdoor into the Ivy League for low scoring blacks.
Even if teachers are being honest, a “survey” of their opinions about why some kids aren’t as smart as others is hardly a scientific inquiry.
All the alleged causative factors could be confirmed or ruled out by properly designed studies that held other factors constant.
But yet it never fails, the fallback answer is always to blame some mystery factor that can’t be identified, but that also has some rough correlation to income. Gee, what could it be? We’ll just have to keep funding more studies and surveys.
Yeah, I know. It’s an attempt to use a capitalization sometimes instead of lowly lower-cased white, especially next to “Asian.” “European-descent” is ponderous, and “Americans” no longer means the same. Using “European-Americans” is giving in to the notion that the majority is merely another subgroup, and “White” is simply incorrect (as is “Black.”) So, “Caucasians” for now. Suggestions welcome.
So 9% of the polled teachers believe that Asian-white differences are significantly genetic, but don’t think the same about white-black differences?
I wonder how they square that circle.
They square that circle by saying "They say this survey is anonymous, I wonder if that's true?"
It’s interesting that she calls the gap “intractable,” which is what Charles Murray calls it. “Do you think the gap is genetic or environmental?” “It’s intractable.”
She says she took it in the 80s and
I assume she means 99th English and 75th Math? It seems unlikely you could get 99th overall w/ only 75th math, but that’s still respectable, so what you say makes some sense.
I’d be curious how she sees herself intelligence wise compared to other black people she interacts with. If there are many she is likely to be quite smart in those groups. Maybe she assume it’s just because she’s more learned and that’s all that’s going on?
(just speaking statistically)
According to this site: https://www.iqcomparisonsite.com/oldSATIQ.aspx
top 1% composite V+M on the pre-1995 SAT was 1300. Between 1270-1280 is the 98.5th percentile which would round up to 99. Does anyone know for sure how the SAT score reports handle rounding of percentiles? I am guessing they are optimistic for everything except for >99.5 since they report numbers from 1-99. Looking at this document:
https://collegereadiness.collegeboard.org/pdf/understanding-sat-scores.pdf
They appear to use 99+ and 1- for >= 99.5 and < 0.5 respectively.
Dorans 2004 is a great reference for SAT 1995 recentering information and 1990 distribution histograms overall and by sex or race.
https://www.ets.org/Media/Research/pdf/RR-02-04-Dorans.pdf
Looking at Figure 15 (use the original scale version on the top) we see that 99th verbal was about 700, 99th math was about 750, and 75th math was around 560-570.
With those numbers a score of 570 math and 730 verbal would give a 99th percentile 1300 composite. That sounds plausible to me, but your interpretation is possible IMHO.
Let's assume 570/700 (even number makes it easier to calculate percentile from histogram, and this would be the rounded 99th percentile composite) and see how she compares with more specific groups. For women (Figure 16) her verbal is still around 99th, but her math is about 85th. For blacks (Figure 18) her verbal becomes 99.9th and her math around 95th.
I share your curiosity.
All the alleged causative factors could be confirmed or ruled out by properly designed studies that held other factors constant.
But yet it never fails, the fallback answer is always to blame some mystery factor that can't be identified, but that also has some rough correlation to income. Gee, what could it be? We'll just have to keep funding more studies and surveys.
The end of the piece quotes a black Harvard economist who has somehow gotten himself christened as an achievement gap expert as saying that the key is early-brain development. This appears to boil down to dialing down the crack and booze during pregnancy, getting really cool mobiles for the crib, and having mom, dad, and the local drag queen read stories to the kid.
The answer for the main question is in the video of professor Robert Plomin’s talk at Google.
While he had no even one sentence on racial difference in educational achievement, after his speech everybody knows the correct answer: if we see afroamerican and white groups as extended families, parents are responsible for the gap trough their inherited genes…
How come they never ask why Northeast Asians perform better then White students.
This woman is obviously an idiot.
Someone commented without reading the article. So who is the idiot now?
Conversely here’s a standard USA Today story on the topic that blames the usual media suspects, racist teachers and society.
https://www.usatoday.com/story/news/education/2020/01/13/nyc-doe-racist-segregation-brooklyn-specialized-high-school-exam-gifted/2763549001/
Evidently the nice white lady author is “troubled” that black and Hispanics parents also oppose eliminating gifted programs:
The real kicker is that the article states unequivocally that cognitive ability is not the reason for the gap, you bigot. She has research!
Well there you have it! It's just a fact, dude. No citations or evidence necessary. Don't believe me? I am 100% prepared to call you racist.
I'd be curious how she sees herself intelligence wise compared to other black people she interacts with. If there are many she is likely to be quite smart in those groups. Maybe she assume it's just because she's more learned and that's all that's going on?
(just speaking statistically)
Her high verbal score might explain why her article is more reasonable and less aggrieved than most these days.
https://www.edweek.org/ew/contributors/christina.samuels.html
She does seem to be something of a true believer in general though:
Poverty, Not Race, Fuels the Achievement Gap
https://www.edweek.org/ew/articles/2019/10/02/poverty-not-race-fuels-the-achievement-gap.html
I guess she doesn't read the JBHE (The Journal of Blacks in Higher Education):
http://www.jbhe.com/latest/index012209_p.html
http://www.jbhe.com/latest/news/1-22-09/satracialgapfigure.gif
P.S. The study she links in that poverty article has a fun disclaimer:
https://edopportunity.org/papers/wp19-06-v092019.pdfAnother fun excerpt:That Nisbett guy must be quite the expert on group differences to be the source of all of her references ; )
Here is the 2012 reference for anyone interested:
https://www.ncbi.nlm.nih.gov/pubmed/22963427
Actually the VOTERS decided teachers are to blame.
The average black IQ in Africa is 68. In the US it is 85. America already works very hard to make blacks 25% smarter–how in the heck could we ever expect better results?
Ms. Samuels late last year reported on a study out of Stanford that put the blame on poverty, so that might be what she is leaning on in her judgment:
https://www.edweek.org/ew/articles/2019/10/02/poverty-not-race-fuels-the-achievement-gap.html
(PDF) https://edopportunity.org/papers/wp19-06-v092019.pdf
The lead author is a white sociologist (all degrees are in education though) who identifies as lowercase, judging by how his, and only his, name is styled in the paper (although most other web references to him do not do this). He holds the endowed Professor of Poverty and Inequality in Education chair at Stanford. Here is some of the stuff he studies, courtesy Wikipedia:
I think this means that blacks and whites tend to live in different school districts or in neighborhoods that result in their kids’ going to different schools. But if you only have an education degree, it’s important to use a lot of obfuscatory jargon in your papers if you want tenure.
If I was a Professor of Poverty I would do my best to make sure that it continued to exist because if poverty disappeared then I would be out of a job and poor myself.
https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0081-1750.2004.00150.x
I am more than a little suspicious that "best" will turn out to be "gave the answers they wanted", but am not motivated to dig further. If anyone else has the fortitude, please report back.
Only White kids from poor families with income of $30k perform better then Black kids from upper-middle income families with income ~$150-200k.
I'd be curious how she sees herself intelligence wise compared to other black people she interacts with. If there are many she is likely to be quite smart in those groups. Maybe she assume it's just because she's more learned and that's all that's going on?
(just speaking statistically)
If she’s telling the truth, she’s smarter than her fellow (often white) reporters. That experience, being smarter than the white people around you in your job, is unusual for a black American. Affirmative Action means that, controlling for level of “success,” the black is usually dumber than the people around him.
American blacks have 20% European ancestry though, which impacts the result.
While he had no even one sentence on racial difference in educational achievement, after his speech everybody knows the correct answer: if we see afroamerican and white groups as extended families, parents are responsible for the gap trough their inherited genes…
https://www.youtube.com/watch?v=-k41lteal1M
Was this at Google in the U.K.?
It’s funny how, compared to most Google Talks, at least at the head office, there were hardly any questions. The Q&A is always the highlight of these Google Talk videos, with brainiac Aspergers Googlers showing off and trying to upstage the speaker with verbose, geeky “questions” that contain no question.
I am imagining that the typical audience member was thinking that Plomin was very problematic, but that “I, as a smart person, do not want to try to go head to head with him on the science because he may be right, actually, he sounds right, and I will look dumb. Is looking dumb better or worse than looking alt-Right? Maybe I will just stay quiet.”
Plomin’s crack about President Clinton was very layered. “Clinton is an example of random environmental input because he said he went into politics because he shook JFK’s hand. But maybe Clinton was lying, in light of his other statements, hahaha.” Audience is thinking: Clinton was a Democrat, so Plomin must be a Nazi Republican! Wait, Clinton put thousands of black bodies of color in prison, so good people hate him … or do they? Oh, I’m so confused!
But if I were Plomin, I’d get rid of the Clinton crack just to be on the safe side.
I wonder how they square that circle.
I wonder how they square that circle.
They square that circle by saying “They say this survey is anonymous, I wonder if that’s true?”
Who’s to blame for the apples-oranges gap?
Who’s to blame for the alligator-pineapple gap?
There is no black-white achievement gap, and there never was, and there never will be. Blacks achieve precisely what they are able to achieve, as do Whites. Better to look at differences within respective groups, for clues to improvement, if there can be any.
If “racism” (which is now a meaningless term except regarding structural hostility to Whites) is to blame for the alleged black-White “achievement” gap, then is racism also to blame for the even wider black-Jewish gap? Or the smaller but still detectable black-Latino gap?
Besides, there are as many achievement gaps as there are achievements. How can we close the black-Pacific Islander gap in professional leaping about and throwing a rubber ball through a hoop? What about the Latino-Jewish gap in plotting and scheming? Will there continue to be a Jewish-Indian gap in ethno-nepotism, or has that gap already closed? What about the White-Asian gap in cheating at tests? Or the black-Indian gap in raping White girls?
So many gaps, so little time. This is all much easier in Korea.
https://www.usatoday.com/story/news/education/2020/01/13/nyc-doe-racist-segregation-brooklyn-specialized-high-school-exam-gifted/2763549001/
Evidently the nice white lady author is “troubled” that black and Hispanics parents also oppose eliminating gifted programs:The real kicker is that the article states unequivocally that cognitive ability is not the reason for the gap, you bigot. She has research!
“Those divides are not due to cognitive differences between races, but a function of access, resources and systemic bias against blacks and Latinos, education experts said.”
Well there you have it! It’s just a fact, dude. No citations or evidence necessary. Don’t believe me? I am 100% prepared to call you racist.
No, academic performance and IQ are pretty much synonymous on a statistical basis. You can have individuals who over perform or under perform academically based on their IQ but for large groups they are highly correlated.
That may be part of it but only part. The other part is genetic so no amount of hitting the books is going to close 100% of the gap.
But closing say half of it would be nice. But to do that you’d have to do social interventions far beyond what our society would tolerate. Turning a ghetto family into an Asian Tiger family is no small thing. Nothing you do at school is going to help because the kid is with his family 87% of the time.
Many parents today seem to think schools should be responsible for the training of their children. Nothing could be further from the truth. Parental ownership of this task is vital to raising healthy (in body and mind) children.
It's easier to blame "pick your favorite ism" for one's offspring's shortcomings rather than self examination and taking ownership of the means and ways to address said deficiencies.
https://www.edweek.org/ew/articles/2019/10/02/poverty-not-race-fuels-the-achievement-gap.html
(PDF) https://edopportunity.org/papers/wp19-06-v092019.pdf
The lead author is a white sociologist (all degrees are in education though) who identifies as lowercase, judging by how his, and only his, name is styled in the paper (although most other web references to him do not do this). He holds the endowed Professor of Poverty and Inequality in Education chair at Stanford. Here is some of the stuff he studies, courtesy Wikipedia:I think this means that blacks and whites tend to live in different school districts or in neighborhoods that result in their kids' going to different schools. But if you only have an education degree, it's important to use a lot of obfuscatory jargon in your papers if you want tenure.
Wow, back in my day you didn’t need a professor to teach you how to be poor. In fact you could get a job waitressing at the coffee shop without any degree at all. Times have changed, I guess.
If I was a Professor of Poverty I would do my best to make sure that it continued to exist because if poverty disappeared then I would be out of a job and poor myself.
Yes, massa worked very hard on his slave girls to improve their kid’s IQ.
But closing say half of it would be nice. But to do that you'd have to do social interventions far beyond what our society would tolerate. Turning a ghetto family into an Asian Tiger family is no small thing. Nothing you do at school is going to help because the kid is with his family 87% of the time.
I agree with your comment and believe you are 100% correct. Growing up our family never had much money. In spite of our particular familial dysfunction we always had enough to eat and there were always books and magazines around the house. My most cherished heirloom after the passing of our parents was a set of Great Books of the Western World. My father was a prolific reader who always had a couple of books going at any time. A love of reading was instilled in us by example. I had been reading for almost a year prior to entering kindergarten thanks to an older sister who taught me the alphabet and says I just took off from there.
Many parents today seem to think schools should be responsible for the training of their children. Nothing could be further from the truth. Parental ownership of this task is vital to raising healthy (in body and mind) children.
It’s easier to blame “pick your favorite ism” for one’s offspring’s shortcomings rather than self examination and taking ownership of the means and ways to address said deficiencies.
This appears to have been a widely accepted practice in the past: I have a dictionary from the thirties which has numerous charts, graphs, full-color illustrations, brief articles (or at least, entries a bit long for a dictionary), drawings, photographs, technical schematics, flag arrays and historical timelines, so that evenings spent with this one book would basically educate an underschooled person as well as anything else.
I'd be curious how she sees herself intelligence wise compared to other black people she interacts with. If there are many she is likely to be quite smart in those groups. Maybe she assume it's just because she's more learned and that's all that's going on?
(just speaking statistically)
Thanks for following up. Let’s estimate some scores from that information.
According to this site: https://www.iqcomparisonsite.com/oldSATIQ.aspx
top 1% composite V+M on the pre-1995 SAT was 1300. Between 1270-1280 is the 98.5th percentile which would round up to 99. Does anyone know for sure how the SAT score reports handle rounding of percentiles? I am guessing they are optimistic for everything except for >99.5 since they report numbers from 1-99. Looking at this document:
https://collegereadiness.collegeboard.org/pdf/understanding-sat-scores.pdf
They appear to use 99+ and 1- for >= 99.5 and < 0.5 respectively.
Dorans 2004 is a great reference for SAT 1995 recentering information and 1990 distribution histograms overall and by sex or race.
https://www.ets.org/Media/Research/pdf/RR-02-04-Dorans.pdf
Looking at Figure 15 (use the original scale version on the top) we see that 99th verbal was about 700, 99th math was about 750, and 75th math was around 560-570.
With those numbers a score of 570 math and 730 verbal would give a 99th percentile 1300 composite. That sounds plausible to me, but your interpretation is possible IMHO.
Let's assume 570/700 (even number makes it easier to calculate percentile from histogram, and this would be the rounded 99th percentile composite) and see how she compares with more specific groups. For women (Figure 16) her verbal is still around 99th, but her math is about 85th. For blacks (Figure 18) her verbal becomes 99.9th and her math around 95th.
I share your curiosity.
(also thanks for linking that Dorans paper. I remember reading through it some years ago for some reason. It's surprising how much fidelity SAT verbal had on the top end by the end. That recentering (and some of the other changes shortly after it) were definitely a blow to IQ enthusiasts... )
This is untrue. The social definition of White has always closely adhered to the one drop rule. One discernible “drop” of non-white genetics has long traditionally conveyed non-White status. This is sill the case, regardless of the mental masturbation of the media priesthood.
Alternately stated, being White has generally been defined by more by what it isn’t more than by what it is. Which is why most quality “trailer trash” are still and will always be vastly more White than Barack: accounting for both genetics and behavior.
Non-whites frequently don’t grasp the long-standing one drop rule. To the point that it often seems to constitute a type of racial dysmorphia. To wit, I once had a half Pakistani, half White acquaintance, who looked like a young Iron Sheik, tell me that he was White. We aren’t friends now, and so I still sometimes relish the moment of the look on his face when my younger self couldn’t hide the look of reflexive disbelief on my face.
Black is what one gets when they mix all of the colors together. A White surface rejects those colors, as a matter of its continued existence, and reflects them back to their source.
Good point. She might be a good resource for some thoughtful commentary in this area. Here is her contributor page at Education Week:
https://www.edweek.org/ew/contributors/christina.samuels.html
She does seem to be something of a true believer in general though:
Poverty, Not Race, Fuels the Achievement Gap
https://www.edweek.org/ew/articles/2019/10/02/poverty-not-race-fuels-the-achievement-gap.html
I guess she doesn’t read the JBHE (The Journal of Blacks in Higher Education):
http://www.jbhe.com/latest/index012209_p.html
P.S. The study she links in that poverty article has a fun disclaimer:
https://edopportunity.org/papers/wp19-06-v092019.pdf
Another fun excerpt:
That Nisbett guy must be quite the expert on group differences to be the source of all of her references ; )
Here is the 2012 reference for anyone interested:
https://www.ncbi.nlm.nih.gov/pubmed/22963427
https://www.edweek.org/ew/articles/2019/10/02/poverty-not-race-fuels-the-achievement-gap.html
(PDF) https://edopportunity.org/papers/wp19-06-v092019.pdf
The lead author is a white sociologist (all degrees are in education though) who identifies as lowercase, judging by how his, and only his, name is styled in the paper (although most other web references to him do not do this). He holds the endowed Professor of Poverty and Inequality in Education chair at Stanford. Here is some of the stuff he studies, courtesy Wikipedia:I think this means that blacks and whites tend to live in different school districts or in neighborhoods that result in their kids' going to different schools. But if you only have an education degree, it's important to use a lot of obfuscatory jargon in your papers if you want tenure.
Mostly. It looks like they developed a number of different metrics and determined which are best.
https://onlinelibrary.wiley.com/doi/abs/10.1111/j.0081-1750.2004.00150.x
I am more than a little suspicious that “best” will turn out to be “gave the answers they wanted”, but am not motivated to dig further. If anyone else has the fortitude, please report back.
I am not aware of any education writer, Left or Right, famous or obscure, who will publicly cite the number one cause of the gap: I.Q. To my knowledge, identifying I.Q. has been banned. It is an unword.
According to Richard Herrnstein, in I.Q. in the Meritocracy (1968), I.Q. is 81% genetic.
That doesn’t mean that parents, siblings, relatives and neighborhoods aren’t factors, as well, but they are secondary factors.
Also, the author misuses the word “equity.”
Mental testing was never developed, in order to foster “equity,” which as used by the racist Left today means equal results. One motivation was to help slow kids. Another was in order to give poor but brilliant kids, like the Jews who came to dominate CCNY and then Harvard, a chance to compete with rich kids.
https://www.officialasvab.com/history_res.htm
During WWII, my late FIL (who later became an engineer and a corporate president but at the time was just a poor ghetto boy) scored very high on his AGCT and the chaplain of his unit (apparently the only other person who could read without moving his lips so they became friends despite the fact that one was a Christian minister and the other was an atheist of Jewish background) offered to get him into officer candidate school but my FIL knew the life expectancy of 2nd lieutenants and he declined.
I know you are joking Jack, but if admixture were the only factor we would be looking at an average African IQ around 80. Ballpark numbers might be 20% average white admixture giving something like 0.2 * 100 + 0.8 * 81 = 85 (rounded 84.8)
1. "... geneticists agree that we are more different from each other as individuals, than we are as populations grouped by “race.”
This is true. What it means is that although the mean IQ of blacks and whites are a single standard deviation apart, if you look at all blacks, they are spread over four or six or more standard deviations, as are all whites, and these spans mostly overlap.
So for the most part, at any IQ level there are blacks and whites.
However, the 1 SD difference (as well as a narrower variance) means that there are substantially fewer blacks, proportionally to their representation in the population, than whites, at any IQ over about 80, and the higher you go, the more disproportionate things get (and at the extreme right tail blacks disappear altogether).
For instance, 25 percent of whites have IQs over 110 (the old fashioned de facto cutoff for university attendance and the professions), while less than 3 percent of blacks reach that level. Taking current United States race percentages, 62 percent non-Hispanic white and 13 percent black, and simplifying things by assuming that there are only blacks and non-Hispanic whites, a 1,000-member entering class at a university would contain about 980 n-H whites and 20 blacks, if admissions were based on random selection of all applicants reaching a minimum threshold of an IQ of 110, and it would be worse if admissions were done in rank order from the top down.
And yet, indeed, it is still true that "we are more different from each other as individuals, than we are as populations grouped by race."
2. "Yes, it mattered that my parents were middle-class, college-educated folks who filled my childhood home with books."
This will never die, I suppose, but the "book access" theory of IQ has long since been debunked (as has the MSG Chinese restaurant syndrome, but that also lives on in folklore), including by twin studies. Rather than her parents' "filling her home with books," her father "filled her mother's vagina with semen," which, after fertilization gave the writer a genome that created a person with sufficient intelligence to appreciate books and seek them out, just as her parents' genomes motivated them to fill their home with books. If adopted by illiterates at birth, she still would have nagged someone into taking her to the library.
Short of the feral child raised by wolves situation, a smart kid will one way or another get ahold of books, whatever the home situation is, and a dumb kid will ignore books if they are not shoved down his throat, and if shoved down his throat, any effect will fade out within two years.
Possible, perhaps probable, by no means certain. Early childhood is an especially important time for conditioning, which is why culture matters. Intellectual potential has to be formed and nurtured, not all cultures do that.
Maybe, but reading a book is also training to read and comprehend, analyze and critique, and this methodical knowledge is valuable even for non-readers.
These results are from twin and adoption studies, as well as all those Head Start studies. You and I can think and overthink and pontificate and theorize all we want about what is going on inside the black box, but we know what is coming out of the black box, and it's as I characterized it: smart kids reflect their birth parents and are not affected by their adoptive parents at all; and force-fed Head Starters fade after two years. And you can add to this the results that teacher quality does not affect kids: smart kids survive and thrive despite crappy teachers and dumb kids are forever dumb, even with award winning teachers.
It's discouraging and creepy and it makes us feel like deterministic automatons. It takes some of the joy and pain out of parenting.
But it is true, for better or worse.
Well there you have it! It's just a fact, dude. No citations or evidence necessary. Don't believe me? I am 100% prepared to call you racist.
These lefty woke ass-wipes have been running the system for decades now, and claim at the same time that it’s biased because of evil white supremacy. Time to kick them out of the system.
Many parents today seem to think schools should be responsible for the training of their children. Nothing could be further from the truth. Parental ownership of this task is vital to raising healthy (in body and mind) children.
It's easier to blame "pick your favorite ism" for one's offspring's shortcomings rather than self examination and taking ownership of the means and ways to address said deficiencies.
Even that is overrated. Growing up, there were few of either in my house (at least not in English) that we actually owned. But they took me to the library a lot. By the time I was in high school I got a few magazine subscriptions but to this day I don’t see the value of owning books for myself (other than reference works). I read a novel and I am done with it. It’s just more clutter after that.
According to Richard Herrnstein, in I.Q. in the Meritocracy (1968), I.Q. is 81% genetic.
That doesn't mean that parents, siblings, relatives and neighborhoods aren't factors, as well, but they are secondary factors.
Also, the author misuses the word "equity."
Mental testing was never developed, in order to foster "equity," which as used by the racist Left today means equal results. One motivation was to help slow kids. Another was in order to give poor but brilliant kids, like the Jews who came to dominate CCNY and then Harvard, a chance to compete with rich kids.
IQ testing was largely developed by the military which needed a way to sort the cannon fodder from those who could be trained for more high level killing tasks.
https://www.officialasvab.com/history_res.htm
During WWII, my late FIL (who later became an engineer and a corporate president but at the time was just a poor ghetto boy) scored very high on his AGCT and the chaplain of his unit (apparently the only other person who could read without moving his lips so they became friends despite the fact that one was a Christian minister and the other was an atheist of Jewish background) offered to get him into officer candidate school but my FIL knew the life expectancy of 2nd lieutenants and he declined.
Many parents today seem to think schools should be responsible for the training of their children. Nothing could be further from the truth. Parental ownership of this task is vital to raising healthy (in body and mind) children.
It's easier to blame "pick your favorite ism" for one's offspring's shortcomings rather than self examination and taking ownership of the means and ways to address said deficiencies.
I try to give good educational, factual books with bite-sized readings as gifts to related children, following George MacDonald Fraser’s claim that his real education came from irregularly nibbling an excellent children’s encyclopedia set. Of course a children’s encyclopedia in Fraser’s childhood would today be seen as interchangeable with Mein Kampf. I settled on the earliest edition of Hirsch’s First Dictionary of Cultural Literacy (which came out in the early 90s and is reasonably unwoke for today) but I hope to find a cheap multi-volume set which would be anything like what Fraser had, giving greater depth.
This appears to have been a widely accepted practice in the past: I have a dictionary from the thirties which has numerous charts, graphs, full-color illustrations, brief articles (or at least, entries a bit long for a dictionary), drawings, photographs, technical schematics, flag arrays and historical timelines, so that evenings spent with this one book would basically educate an underschooled person as well as anything else.
The ESSA might make it easier to create unqualified teachers, but there’s been no sign of it yet. New York hasn’t dumbed down anything to do with subject matter knowledge.
1. "... geneticists agree that we are more different from each other as individuals, than we are as populations grouped by “race.”
This is true. What it means is that although the mean IQ of blacks and whites are a single standard deviation apart, if you look at all blacks, they are spread over four or six or more standard deviations, as are all whites, and these spans mostly overlap.
So for the most part, at any IQ level there are blacks and whites.
However, the 1 SD difference (as well as a narrower variance) means that there are substantially fewer blacks, proportionally to their representation in the population, than whites, at any IQ over about 80, and the higher you go, the more disproportionate things get (and at the extreme right tail blacks disappear altogether).
For instance, 25 percent of whites have IQs over 110 (the old fashioned de facto cutoff for university attendance and the professions), while less than 3 percent of blacks reach that level. Taking current United States race percentages, 62 percent non-Hispanic white and 13 percent black, and simplifying things by assuming that there are only blacks and non-Hispanic whites, a 1,000-member entering class at a university would contain about 980 n-H whites and 20 blacks, if admissions were based on random selection of all applicants reaching a minimum threshold of an IQ of 110, and it would be worse if admissions were done in rank order from the top down.
And yet, indeed, it is still true that "we are more different from each other as individuals, than we are as populations grouped by race."
2. "Yes, it mattered that my parents were middle-class, college-educated folks who filled my childhood home with books."
This will never die, I suppose, but the "book access" theory of IQ has long since been debunked (as has the MSG Chinese restaurant syndrome, but that also lives on in folklore), including by twin studies. Rather than her parents' "filling her home with books," her father "filled her mother's vagina with semen," which, after fertilization gave the writer a genome that created a person with sufficient intelligence to appreciate books and seek them out, just as her parents' genomes motivated them to fill their home with books. If adopted by illiterates at birth, she still would have nagged someone into taking her to the library.
Short of the feral child raised by wolves situation, a smart kid will one way or another get ahold of books, whatever the home situation is, and a dumb kid will ignore books if they are not shoved down his throat, and if shoved down his throat, any effect will fade out within two years.
>Short of the feral child raised by wolves situation, a smart kid will one way or another get ahold of books, whatever the home situation is, and a dumb kid will ignore books if they are not shoved down his throat, and if shoved down his throat, any effect will fade out within two years.
Don’t throw the baby out with the bathwater. The smart kid might get a hold on books, but he usually won’t learn or use his intelligence properly if not trained when not sufficiently mature, and the converse is true as well.
Practice does make you smarter. It doesn’t override biology, like the blank-slatists would have it. If taken to extremes that all that matters is effort, it can downright nasty: there’s this one Chinese former prodigy doing genetics research who is determined to conclusively prove the role of biology in intelligence specifically to stop parents from ruining their kids lives in the conviction that with enough practice, they can become Gauss or Beethoven. But practice does have a role in making you less dumb, no matter what your biological range is. We have an attitude that there’s no point to seriously understanding mathematics if you can’t be a superstar at it, and it is utterly toxic for the future of the United States. This does matter more than people think. It is a massive quality of life difference to have daily tasks performed by people with IQs of 100 or 105 over 80 or 85, if you are starting out from a base level of 90.
Your parents and your state can’t play God and dictate your genetics (and I hope we don’t get to the point that they can!) but they can play a role in ensuring you’d do 15, 20% better than you normally would. And if done on a society-wide level, it can make a massive difference in your nation’s fate.
Jack D – that being true then one can give the answer that the gap is due to the gap in IQ test scores between the races. Let them mull over what causes those different test scores.
“the black-white achievement gap”
As usual, the whole thing than be explained by Mister Oscar Wilde….
“The rage of Caliban at seeing his own face in a looking glass.”
It’s also not clear that BHO got into Columbia College. I’d bet money that he got into Columbia’s General Studies, which is much different. The only evidence for BHO’s smarts is his ability to read a teleprompter well.
How about “person of little pigmentation”?
The test score gap between “rich” and poor blacks, like the one between rich and poor whites, is actually bigger than the gap between blacks and whites. So it follows that the gap between blacks and whites is largely (if not entirely) a consequence of wealth differences between the races. The whole bit about “high income” blacks scoring worse than poor whites ignores the reality that “high income” blacks typically live in low income neighborhoods and have much less wealth (income – expenses) than poor whites. But who cares about facts? It’s probably our natural inclination to search for tribal advantages over groups that we perceive to be hostile towards our own, as believing in such advantage gives us a sense of security.
You're kidding, right? You just wanted to see if anyone was paying attention.
- Differences in saving/investing volume and effectiveness.
- Differences in overall work history (e.g. duration of the high income).
- Differences in spending habits.
- Differences in family support and inheritances.
The high income blacks in low income neighborhoods idea really needs a citation though. For those who care about facts, anyway.
BTW, living in a low income neighborhood should tend to reduce expenses both directly and by reducing the need to "keep up with the Joneses."
Do you have a cite for a study showing high income blacks have less wealth than low income whites? Depending on what "high" and "low" mean that is possible, but it would be better to have real data.Very few who try to pretend there is no test score gap OR it is purely environmental in origin. And providing references is a good sign of who truly cares about facts. You might compare our comments in that respect.
P.S. I looked around a bit and this seems like a pretty good study indicating the current wealth gap is mostly due to income differences:
https://www.citylab.com/equity/2019/03/racial-wealth-gap-income-inequality-black-white-households/585325/
More at
https://www.clevelandfed.org/newsroom-and-events/publications/economic-commentary/2019-economic-commentaries/ec-201903-what-is-behind-the-persistence-of-the-racial-wealth-gap.aspx
https://web.archive.org/web/20190405152704/http://dionissialiprantis.com/pdfs/dynamics_RWG_07_27.pdf
https://cdn.theatlantic.com/assets/media/img/posts/2019/03/racial_wealth_gap_chart_1/df7592ddc.png
The whole bit about “high income” blacks scoring worse than poor whites ignores the reality that “high income” blacks typically live in low income neighborhoods and have much less wealth (income – expenses) than poor whites. But who cares about facts?
That’s speculation, not facts.
It’s probably our natural inclination to search for tribal advantages over groups that we perceive to be hostile towards our own, as believing in such advantage gives us a sense of security.
It’s egalitarians that are obsessed with closing the gap. Or do you think that racist Whites are the ones that have supported the billions spent on proposed solutions?
Yes in the mind of the egalitarian anyone that questions their great effort to equalize everyone must be a wayciss. Nevermind that their great solution called NCLB actually ended up cutting funding for Black schools since both Republicans and Democrats were convinced the gap was artificial.
I was against NCLB because I knew it would cut funding to poor schools. I was right and the liberals with good intentions and PHds in Education were wrong. I would have increased funding to Black schools but without this bizarre expectation that all groups should do exactly the same. Do we have that expectation in sports? Why not?
I give Slimer credit for the rhetorical agility he demonstrates in working two baseless howlers into a single sentence.
One more addition which is that the gap is worse than depicted.
They have methods for skewing the data even if it is regulated.
I’m not going to discuss them here.
I don’t really care for either side and I don’t want to encourage any liberal principal or teacher that is unaware of the tactics.
According to this site: https://www.iqcomparisonsite.com/oldSATIQ.aspx
top 1% composite V+M on the pre-1995 SAT was 1300. Between 1270-1280 is the 98.5th percentile which would round up to 99. Does anyone know for sure how the SAT score reports handle rounding of percentiles? I am guessing they are optimistic for everything except for >99.5 since they report numbers from 1-99. Looking at this document:
https://collegereadiness.collegeboard.org/pdf/understanding-sat-scores.pdf
They appear to use 99+ and 1- for >= 99.5 and < 0.5 respectively.
Dorans 2004 is a great reference for SAT 1995 recentering information and 1990 distribution histograms overall and by sex or race.
https://www.ets.org/Media/Research/pdf/RR-02-04-Dorans.pdf
Looking at Figure 15 (use the original scale version on the top) we see that 99th verbal was about 700, 99th math was about 750, and 75th math was around 560-570.
With those numbers a score of 570 math and 730 verbal would give a 99th percentile 1300 composite. That sounds plausible to me, but your interpretation is possible IMHO.
Let's assume 570/700 (even number makes it easier to calculate percentile from histogram, and this would be the rounded 99th percentile composite) and see how she compares with more specific groups. For women (Figure 16) her verbal is still around 99th, but her math is about 85th. For blacks (Figure 18) her verbal becomes 99.9th and her math around 95th.
I share your curiosity.
Thanks for working that out. My statement was just at the hunch level. Since you show that 700-730V / 570M fits what she literally wrote there’s much less reason to doubt it’s what she meant, even if it’s a little strange to report V+M and M instead of all three or just total or just components.
(also thanks for linking that Dorans paper. I remember reading through it some years ago for some reason. It’s surprising how much fidelity SAT verbal had on the top end by the end. That recentering (and some of the other changes shortly after it) were definitely a blow to IQ enthusiasts… )
Even that answer is more acceptable than the more accurate one.
Darwin.
http://i.imgur.com/xo2v8Zd.pngSo, we should be satisfied that they don’t call hereditarians evil racists all the while they ignore the obvious hereditarian evidences.
She’s writing under her own name in a publication where the genetic explanation of racial IQ differences is roughly as socially acceptable as getting a “666” tattoo on your forehead, and she’s still playing fair with the facts. That’s better than like 99% of people manage on this topic.
I wonder how they square that circle.
I think in NYC, Asians are much poorer than whites on average, yet do much better on magnet entrance exams. Richer whites outperforming poorer blacks looks like it might be environmental; richer whites being outperformed by poorer Asians probably looks more plausibly genetic.
i make it through answering where i'm not frustrated by the ambiguity of the questions and answer choices. )
These results are from twin and adoption studies, as well as all those Head Start studies. You and I can think and overthink and pontificate and theorize all we want about what is going on inside the black box, but we know what is coming out of the black box, and it’s as I characterized it: smart kids reflect their birth parents and are not affected by their adoptive parents at all; and force-fed Head Starters fade after two years. And you can add to this the results that teacher quality does not affect kids: smart kids survive and thrive despite crappy teachers and dumb kids are forever dumb, even with award winning teachers.
It’s discouraging and creepy and it makes us feel like deterministic automatons. It takes some of the joy and pain out of parenting.
But it is true, for better or worse.
Yeah, i guess that if you don’t know about existence of studies that (attempt to) correct for those things and the history of failed interventions (which many of the respondents probably don’t) then it makes sense.
Or it could be the rank of significance in the view of the respondent e.g. it’s the top-factor in case “a” but only third in case “b”.
(it’s a rare opinion survey (or diagnostic questionnaire)
i make it through answering where i’m not frustrated by the ambiguity of the questions and answer choices. )
It was just as bad in the 1960s. In fact, Detroit’s Northeastern High School had a “black students union” that was successful in getting the American flag removed from the front of the school and replacing it with a “black nationalist” flag.
The ordeal that us white students had to go through was harrowing, to say the least. White students did not use the restrooms, as a “beatdown” by multiple blacks was usually the result.
Blacks never fought one-on-one, the “pack mentality” was evident then as is today.
Any attempts by whites to defend themselves was met with indifference, and even outright hostility from school officials. You see, even then, blacks were not “responsible” for their behavior.
Blacks did not want to learn, the same situation that still exists today. Even then, blacks were disruptive. Most of the teachers just shrugged their shoulders, let the disruptions go on until the next class period.
Teachers were deferential to blacks, although there were a few teachers who tried to carefully shield their white and asian students from predatory blacks, giving them additional attention and coursework, knowing that they could excel in spite of the, violent, raucous atmosphere.
Anywhere blacks go, they destroy…
The whole bit about “high income” blacks scoring worse than poor whites ignores the reality that “high income” blacks typically live in low income neighborhoods and have much less wealth (income – expenses) than poor whites.
I give Slimer credit for the rhetorical agility he demonstrates in working two baseless howlers into a single sentence.
These results are from twin and adoption studies, as well as all those Head Start studies. You and I can think and overthink and pontificate and theorize all we want about what is going on inside the black box, but we know what is coming out of the black box, and it's as I characterized it: smart kids reflect their birth parents and are not affected by their adoptive parents at all; and force-fed Head Starters fade after two years. And you can add to this the results that teacher quality does not affect kids: smart kids survive and thrive despite crappy teachers and dumb kids are forever dumb, even with award winning teachers.
It's discouraging and creepy and it makes us feel like deterministic automatons. It takes some of the joy and pain out of parenting.
But it is true, for better or worse.
You have a point, but this dramatically overstates the case. There’s not that much that a talented teacher can do with dim kids, true enough. As far as smart kids surviving, even cows survive; thriving is another matter.
Right, it’s a good article.
See Wm. Dyer on this subject. The distribution of honors at Harvard Law School is through blindly graded examinations. He did well there. He just wasn’t interested in law (or, really, much else).
“The whole bit about ‘high income’ blacks scoring worse than poor whites ignores the reality that ‘high income’ blacks typically live in low income neighborhoods and have much less wealth (income – expenses) than poor whites.”
You’re kidding, right? You just wanted to see if anyone was paying attention.
The ordeal that us white students had to go through was harrowing, to say the least. White students did not use the restrooms, as a “beatdown” by multiple blacks was usually the result.
Blacks never fought one-on-one, the “pack mentality” was evident then as is today.
Any attempts by whites to defend themselves was met with indifference, and even outright hostility from school officials. You see, even then, blacks were not "responsible" for their behavior.
Blacks did not want to learn, the same situation that still exists today. Even then, blacks were disruptive. Most of the teachers just shrugged their shoulders, let the disruptions go on until the next class period.
Teachers were deferential to blacks, although there were a few teachers who tried to carefully shield their white and asian students from predatory blacks, giving them additional attention and coursework, knowing that they could excel in spite of the, violent, raucous atmosphere.
Anywhere blacks go, they destroy…
That’s why we must have racially integrated schools!
The wealth difference (overall, and I think at equal incomes) is well established. I have yet to see a thorough study trying to break down the causes of that and their relative importance though (see below though, I think I found one). Some possibilities.
– Differences in saving/investing volume and effectiveness.
– Differences in overall work history (e.g. duration of the high income).
– Differences in spending habits.
– Differences in family support and inheritances.
The high income blacks in low income neighborhoods idea really needs a citation though. For those who care about facts, anyway.
BTW, living in a low income neighborhood should tend to reduce expenses both directly and by reducing the need to “keep up with the Joneses.”
Do you have a cite for a study showing high income blacks have less wealth than low income whites? Depending on what “high” and “low” mean that is possible, but it would be better to have real data.
Very few who try to pretend there is no test score gap OR it is purely environmental in origin. And providing references is a good sign of who truly cares about facts. You might compare our comments in that respect.
P.S. I looked around a bit and this seems like a pretty good study indicating the current wealth gap is mostly due to income differences:
https://www.citylab.com/equity/2019/03/racial-wealth-gap-income-inequality-black-white-households/585325/
More at
https://www.clevelandfed.org/newsroom-and-events/publications/economic-commentary/2019-economic-commentaries/ec-201903-what-is-behind-the-persistence-of-the-racial-wealth-gap.aspx
https://web.archive.org/web/20190405152704/http://dionissialiprantis.com/pdfs/dynamics_RWG_07_27.pdf
Given that what you call “blacks” have the highest genetic diversity and also the way mutational load is distributed across human populations, why can they not have the highest IQ?
Where is the genetic evidence that “whites” have higher IQ than “blacks”?
Are there any papers that show differential selection pressures in African and European populations? Or that there has been enough isolation to make possible that such differences might exist even due to only soft polygenic selection or drift (unlikely as that would be for other reasons)?
Lots of psychology but not enough genetics in my opinion.
As for who is to blame for the gap: social processes and factors imo.
And who says pigs can't fly anyway. Can you prove that?Piffer's work looking at EDU PGS scores is one piece:
https://www.researchgate.net/publication/332076417_Evidence_for_Recent_Polygenic_Selection_on_Educational_Attainment_and_Intelligence_Inferred_from_Gwas_Hits_A_Replication_of_Previous_Findings_Using_Recent_Data
https://www.mdpi.com/psych/psych-01-00005/article_deploy/html/images/psych-01-00005-g002-550.jpg
And another from admixture analysis:
Global Ancestry and Cognitive Ability
https://emilkirkegaard.dk/en/?p=7995
https://www.unz.com/isteve/global-ancestry-and-cognitive-ability/
https://www.unz.com/wp-content/uploads/2019/09/Screenshot-2019-09-05-02.00.14.png
And here is evidence that Jews have an average genetic IQ higher than that of whites:
FAQ for Dunkel et al 2019 Ashkenazim polygenic score for intelligence
https://emilkirkegaard.dk/en/?p=7680
https://emilkirkegaard.dk/en/wp-content/uploads/bell-curves.pngYes. Here is one looking at multiple traits for European, Asian, and African populations.
Detecting polygenic adaptation in admixture graphs
https://www.biorxiv.org/content/10.1101/146043v1How exactly does "soft polygenic selection" differ from plain old selection?
Does the question of selection or drift really matter here? What we care about is that there are phenotypic differences which appear to have a genetic component. And are you honestly trying to claim that intelligence is not selected for given the trend in hominid brain size over the last few million years?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385680/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385680/bin/rstb20120115-g1.jpgAs opposed to the genetic arguments you brought to this conversation? But feel free to cite another Templeton paper which proves...something or other. Or invoke your sacred "gene flow" or "isolation by distance" answers to everything.Just keep telling yourself that is all there is. That's likely part of the issue, but based on the evidence above (both this comment and the rest of the thread) probably not all.
P.S. I think we have covered this in multiple threads in James Thompson's blog. Please stop with the playing dumb schtick.
Darwin.
Seems you have not read enough about how selection and drift (latter term being from the Neutral theory of molecular evolution-much after Darwin) work.
Because they don’t observationally? But keep looking. You will be a hero if you find an exception.
And who says pigs can’t fly anyway. Can you prove that?
Piffer’s work looking at EDU PGS scores is one piece:
https://www.researchgate.net/publication/332076417_Evidence_for_Recent_Polygenic_Selection_on_Educational_Attainment_and_Intelligence_Inferred_from_Gwas_Hits_A_Replication_of_Previous_Findings_Using_Recent_Data
And another from admixture analysis:
Global Ancestry and Cognitive Ability
https://emilkirkegaard.dk/en/?p=7995
https://www.unz.com/isteve/global-ancestry-and-cognitive-ability/
And here is evidence that Jews have an average genetic IQ higher than that of whites:
FAQ for Dunkel et al 2019 Ashkenazim polygenic score for intelligence
https://emilkirkegaard.dk/en/?p=7680
Yes. Here is one looking at multiple traits for European, Asian, and African populations.
Detecting polygenic adaptation in admixture graphs
https://www.biorxiv.org/content/10.1101/146043v1
How exactly does “soft polygenic selection” differ from plain old selection?
Does the question of selection or drift really matter here? What we care about is that there are phenotypic differences which appear to have a genetic component. And are you honestly trying to claim that intelligence is not selected for given the trend in hominid brain size over the last few million years?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385680/
As opposed to the genetic arguments you brought to this conversation? But feel free to cite another Templeton paper which proves…something or other. Or invoke your sacred “gene flow” or “isolation by distance” answers to everything.
Just keep telling yourself that is all there is. That’s likely part of the issue, but based on the evidence above (both this comment and the rest of the thread) probably not all.
P.S. I think we have covered this in multiple threads in James Thompson’s blog. Please stop with the playing dumb schtick.
You often mention health disparities for example being due to genetics (I am not sure if it was you or one of the other commenters on the Thompson thread) when social factors can indeed better explain them:
https://www.annualreviews.org/doi/10.1146/annurev-publhealth-040119-094017Be serious. I cite a paper for every thing I say, there is nothing that prevents human populations to differ on genotypic IQ, there is just not good evidence they do by race.:
Once again, Piffer did not control for population stratification or even false positives.I will read this one more in depth and get back to you.https://osf.io/preprints/socarxiv/eh9tq/
"We demonstrate instead--and perhaps counterintuitively--that the difference between Jewish and non-Jewish polygenic scores are much too large for their analysis to offer any evidentiary value for this conclusion. Instead, the data show clear evidence of the problems with comparing polygenic scores across ethnic groups that others have noted."It is harder to detect and distinguish for drift. However, if it has taken place then it is the only way I can think of that the hereditarian hypothesis is correct.
In fact, it is what Emil et al are looking for.
I only meant that there is no evidence for hard selection like for lighter skin color in Europeans, which would also make some amount of gene flow irrelevant.Well yes. In the absence of selection we would not expect big differences in IQ genes between human populations. See this paper for example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516610/
Researchers in many fields have considered the meaning of two results about genetic variation for
concepts of “race.” First, at most genetic loci, apportionments of human genetic diversity find that
worldwide populations are genetically similar. Second, when multiple genetic loci are examined, it
is possible to distinguish people with ancestry from different geographical regions. These two
results raise an important question about human phenotypic diversity: To what extent do
populations typically differ on phenotypes determined by multiple genetic loci? It might be
expected that such phenotypes follow the pattern of similarity observed at individual loci.
Alternatively, because they have a multilocus genetic architecture, they might follow the pattern of
greater differentiation suggested by multilocus ancestry inference. To address the question, we
extend a well-known classification model of Edwards (2003) by adding a selectively neutral
quantitative trait. Using the extended model, we show, in line with previous work in quantitative
genetics, that regardless of how many genetic loci influence the trait, one neutral trait is
approximately as informative about ancestry as a single genetic locus. The results support the
relevance of single-locus genetic-diversity partitioning for predictions about phenotypic diversityYou are right. There has been selection for intelligence etc over the last few million years.
My objection is that it has not been different in people of European descent (whatever that means) and African descent.Gene flow spreads variants around. How can you not know this? It also counteracts drift.
Papers that show isolation contra Templeton's analysis would convince me more than just saying it is irrelevant. Did you test that cophenetic correlation you were talking about?
And just so you know, I have no issue admitting I am wrong on something. For example, one of the papers I posted about recent gene flow between Europeans and East Asians apparently was not accurate due to the groups included in the analysis.Do you not get how that creates false positives in association analyses like those for height and many other traits?
https://www.biorxiv.org/content/10.1101/659235v2
(If you have limited time, the above paper is of particular significance to the issue)Not really. I have not seen any quantitative points that rebut my arguments.
https://www.biorxiv.org/content/10.1101/423632v2
And who says pigs can't fly anyway. Can you prove that?Piffer's work looking at EDU PGS scores is one piece:
https://www.researchgate.net/publication/332076417_Evidence_for_Recent_Polygenic_Selection_on_Educational_Attainment_and_Intelligence_Inferred_from_Gwas_Hits_A_Replication_of_Previous_Findings_Using_Recent_Data
https://www.mdpi.com/psych/psych-01-00005/article_deploy/html/images/psych-01-00005-g002-550.jpg
And another from admixture analysis:
Global Ancestry and Cognitive Ability
https://emilkirkegaard.dk/en/?p=7995
https://www.unz.com/isteve/global-ancestry-and-cognitive-ability/
https://www.unz.com/wp-content/uploads/2019/09/Screenshot-2019-09-05-02.00.14.png
And here is evidence that Jews have an average genetic IQ higher than that of whites:
FAQ for Dunkel et al 2019 Ashkenazim polygenic score for intelligence
https://emilkirkegaard.dk/en/?p=7680
https://emilkirkegaard.dk/en/wp-content/uploads/bell-curves.pngYes. Here is one looking at multiple traits for European, Asian, and African populations.
Detecting polygenic adaptation in admixture graphs
https://www.biorxiv.org/content/10.1101/146043v1How exactly does "soft polygenic selection" differ from plain old selection?
Does the question of selection or drift really matter here? What we care about is that there are phenotypic differences which appear to have a genetic component. And are you honestly trying to claim that intelligence is not selected for given the trend in hominid brain size over the last few million years?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385680/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385680/bin/rstb20120115-g1.jpgAs opposed to the genetic arguments you brought to this conversation? But feel free to cite another Templeton paper which proves...something or other. Or invoke your sacred "gene flow" or "isolation by distance" answers to everything.Just keep telling yourself that is all there is. That's likely part of the issue, but based on the evidence above (both this comment and the rest of the thread) probably not all.
P.S. I think we have covered this in multiple threads in James Thompson's blog. Please stop with the playing dumb schtick.
Why do you think that what you observe socially is tied to genetic factors?
You often mention health disparities for example being due to genetics (I am not sure if it was you or one of the other commenters on the Thompson thread) when social factors can indeed better explain them:
https://www.annualreviews.org/doi/10.1146/annurev-publhealth-040119-094017
Be serious. I cite a paper for every thing I say, there is nothing that prevents human populations to differ on genotypic IQ, there is just not good evidence they do by race.
Once again, Piffer did not control for population stratification or even false positives.
I will read this one more in depth and get back to you.
https://osf.io/preprints/socarxiv/eh9tq/
“We demonstrate instead–and perhaps counterintuitively–that the difference between Jewish and non-Jewish polygenic scores are much too large for their analysis to offer any evidentiary value for this conclusion. Instead, the data show clear evidence of the problems with comparing polygenic scores across ethnic groups that others have noted.”
It is harder to detect and distinguish for drift. However, if it has taken place then it is the only way I can think of that the hereditarian hypothesis is correct.
In fact, it is what Emil et al are looking for.
I only meant that there is no evidence for hard selection like for lighter skin color in Europeans, which would also make some amount of gene flow irrelevant.
Well yes. In the absence of selection we would not expect big differences in IQ genes between human populations. See this paper for example: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516610/
Researchers in many fields have considered the meaning of two results about genetic variation for
concepts of “race.” First, at most genetic loci, apportionments of human genetic diversity find that
worldwide populations are genetically similar. Second, when multiple genetic loci are examined, it
is possible to distinguish people with ancestry from different geographical regions. These two
results raise an important question about human phenotypic diversity: To what extent do
populations typically differ on phenotypes determined by multiple genetic loci? It might be
expected that such phenotypes follow the pattern of similarity observed at individual loci.
Alternatively, because they have a multilocus genetic architecture, they might follow the pattern of
greater differentiation suggested by multilocus ancestry inference. To address the question, we
extend a well-known classification model of Edwards (2003) by adding a selectively neutral
quantitative trait. Using the extended model, we show, in line with previous work in quantitative
genetics, that regardless of how many genetic loci influence the trait, one neutral trait is
approximately as informative about ancestry as a single genetic locus. The results support the
relevance of single-locus genetic-diversity partitioning for predictions about phenotypic diversity
You are right. There has been selection for intelligence etc over the last few million years.
My objection is that it has not been different in people of European descent (whatever that means) and African descent.
Gene flow spreads variants around. How can you not know this? It also counteracts drift.
Papers that show isolation contra Templeton’s analysis would convince me more than just saying it is irrelevant. Did you test that cophenetic correlation you were talking about?
And just so you know, I have no issue admitting I am wrong on something. For example, one of the papers I posted about recent gene flow between Europeans and East Asians apparently was not accurate due to the groups included in the analysis.
Do you not get how that creates false positives in association analyses like those for height and many other traits?
https://www.biorxiv.org/content/10.1101/659235v2
(If you have limited time, the above paper is of particular significance to the issue)
Not really. I have not seen any quantitative points that rebut my arguments.
And who says pigs can't fly anyway. Can you prove that?Piffer's work looking at EDU PGS scores is one piece:
https://www.researchgate.net/publication/332076417_Evidence_for_Recent_Polygenic_Selection_on_Educational_Attainment_and_Intelligence_Inferred_from_Gwas_Hits_A_Replication_of_Previous_Findings_Using_Recent_Data
https://www.mdpi.com/psych/psych-01-00005/article_deploy/html/images/psych-01-00005-g002-550.jpg
And another from admixture analysis:
Global Ancestry and Cognitive Ability
https://emilkirkegaard.dk/en/?p=7995
https://www.unz.com/isteve/global-ancestry-and-cognitive-ability/
https://www.unz.com/wp-content/uploads/2019/09/Screenshot-2019-09-05-02.00.14.png
And here is evidence that Jews have an average genetic IQ higher than that of whites:
FAQ for Dunkel et al 2019 Ashkenazim polygenic score for intelligence
https://emilkirkegaard.dk/en/?p=7680
https://emilkirkegaard.dk/en/wp-content/uploads/bell-curves.pngYes. Here is one looking at multiple traits for European, Asian, and African populations.
Detecting polygenic adaptation in admixture graphs
https://www.biorxiv.org/content/10.1101/146043v1How exactly does "soft polygenic selection" differ from plain old selection?
Does the question of selection or drift really matter here? What we care about is that there are phenotypic differences which appear to have a genetic component. And are you honestly trying to claim that intelligence is not selected for given the trend in hominid brain size over the last few million years?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385680/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3385680/bin/rstb20120115-g1.jpgAs opposed to the genetic arguments you brought to this conversation? But feel free to cite another Templeton paper which proves...something or other. Or invoke your sacred "gene flow" or "isolation by distance" answers to everything.Just keep telling yourself that is all there is. That's likely part of the issue, but based on the evidence above (both this comment and the rest of the thread) probably not all.
P.S. I think we have covered this in multiple threads in James Thompson's blog. Please stop with the playing dumb schtick.
Oh and regarding continuous clines and PCAs that you asked me a while back:
https://www.biorxiv.org/content/10.1101/423632v2
It would also be helpful to include a link back to our earlier conversation you want to revisit.
Doing those things would go a long way towards convincing me:
1. You have coherent and sincere arguments.
2. You are interested in having a sincere discussion.
3. It is worth spending time engaging with you.
So far my tentative answer to all 3 is no.
I am still trying to decide whether it is worth responding to your comment 92. I have better things to do than engage in endless back and forth going nowhere with you.
https://www.biorxiv.org/content/10.1101/423632v2
Your point being? Remember when I asked you to include relevant excerpts and the point you think they make? Please stop just dropping links and expecting me to infer your meaning.
It would also be helpful to include a link back to our earlier conversation you want to revisit.
Doing those things would go a long way towards convincing me:
1. You have coherent and sincere arguments.
2. You are interested in having a sincere discussion.
3. It is worth spending time engaging with you.
So far my tentative answer to all 3 is no.
I am still trying to decide whether it is worth responding to your comment 92. I have better things to do than engage in endless back and forth going nowhere with you.
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3644981 was one of my "coherent arguments" for example.I did that in the last thread but you never responded. Still, fair point so I will do so here.
You asked me a while back to show you a PCA that when sampling enough populations shows clines instead of races or clusters.Among another publication from a lab I cited earlier, I think this paper is interesting to show this. See for example the PCAs presented in the figures (particularly figure 4a) and the following text segments:The 1KGP sampled individuals from relatively distinct 110 population groups across the world, which makes the data particularly easy to cluster. Most medical cohorts comprise larger numbers of individuals sampled across extended geographical areas...We have scaled these three proportions to values between 120 and 255, to color individual points by their estimated admixture represented by RGB where red, green, and blue respectively correspond to African, European, and Asian/Native American ancestry. Using the first 10 principal components and UMAP, we demonstrate projections that present a collection of sub-populations and a continuum of genetic variation.
1. I will try to make them more coherent. They are sincere, I told you before if you quantitatively disprove them I have no issue changing my mind about something. 2. I am. are you? I was not initially true, but when I hear interesting arguments I stick around. I obviously disagree with most of the stuff you believe about race and IQ etc, but will reconsider something if shown to be wrong (like I did with the height stuff, Basal Eurasians being an African population and the paper about recent East Asian-Europe gene flow)3. That is up to you to decide. You will however, hear the same or similar arguments from every other person on the anti-hereditarian side you engage with about race. All the papers and links I have cited are peer-reviewed evidence and arguments used by experts in the field.
It would also be helpful to include a link back to our earlier conversation you want to revisit.
Doing those things would go a long way towards convincing me:
1. You have coherent and sincere arguments.
2. You are interested in having a sincere discussion.
3. It is worth spending time engaging with you.
So far my tentative answer to all 3 is no.
I am still trying to decide whether it is worth responding to your comment 92. I have better things to do than engage in endless back and forth going nowhere with you.
That is of course up to you, but if you think I am wrong then why not show where?
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3644981 was one of my “coherent arguments” for example.
I did that in the last thread but you never responded. Still, fair point so I will do so here.
You asked me a while back to show you a PCA that when sampling enough populations shows clines instead of races or clusters.
Among another publication from a lab I cited earlier, I think this paper is interesting to show this. See for example the PCAs presented in the figures (particularly figure 4a) and the following text segments:
The 1KGP sampled individuals from relatively distinct 110 population groups across the world, which makes the data particularly easy to cluster. Most medical cohorts comprise larger numbers of individuals sampled across extended geographical areas…We have scaled these three proportions to values between 120 and 255, to color individual points by their estimated admixture represented by RGB where red, green, and blue respectively correspond to African, European, and Asian/Native American ancestry. Using the first 10 principal components and UMAP, we demonstrate projections that present a collection of sub-populations and a continuum of genetic variation.
1. I will try to make them more coherent. They are sincere, I told you before if you quantitatively disprove them I have no issue changing my mind about something.
2. I am. are you? I was not initially true, but when I hear interesting arguments I stick around. I obviously disagree with most of the stuff you believe about race and IQ etc, but will reconsider something if shown to be wrong (like I did with the height stuff, Basal Eurasians being an African population and the paper about recent East Asian-Europe gene flow)
3. That is up to you to decide. You will however, hear the same or similar arguments from every other person on the anti-hereditarian side you engage with about race. All the papers and links I have cited are peer-reviewed evidence and arguments used by experts in the field.
https://www.unz.com/isteve/guardian-i-read-angela-sainis-superior-and-the-scales-fell-from-my-eyes/#comment-3643398
When you keep saying the same thing over and over again do you really expect me to respond to each and every comment saying the same thing?Regarding your point 2: "You asked me to find you PCAs that are entirely clinal with no gaps. These PCAs support my argument of entirely clinal variation without any clustering. I did so.https://macarthurlab.org/2019/10/16/gnomad-v3-0/"Let me give a sample of how I would like to see YOU engage. Here is the PCA in question (see how easy it is to include a picture or quote so we can have a concrete discussion without chasing links?):https://macarthurlab.files.wordpress.com/2019/10/ancestry_pca.pngThat PCA is a mass of overplotting which I believe overstates the importance of the clines relative to the clusters. Keep in mind that your assertion was entirely clinal variation without any clustering. You clearly see a few clusters there: Finns, Amish, and Ashkenazi Jewish. You also clearly see the structure as a triangle with the three vertices being East Asian, African, and European (BTW, one interesting thing is how little East Asian/African mixing there is).So you see that your graphic actually does not show what you claimed. It does show some clinal variation. And I have agreed many times that mixed race people exist. But you can clearly see some of those clusters and a better plot showing density in those heavily overplotted areas would make the others more clear.So I expend time, effort, and words to prove you wrong, but will you admit it? I know the answer already (experience is a good teacher), but let's let it play out so others can see. Repeat this process manyfold and maybe you (and anyone else reading this who cares) will see why I am sick of dealing with you. Frankly, I don't care what you think anymore. I just want to make sure no one else here is misled by your misinformation.One weakness of that PCA plot is it fails to show the percent variance explained for the PCs. A notable feature of PCA plots like this (at least the better ones which include that critical information) is just how much of the genetic variance is explained by those two PCs. In particular PC1 corresponding to the European-African variation.Here is Figure 4a. See how easy this is?https://www.biorxiv.org/content/biorxiv/early/2019/03/16/423632/F4.large.jpgThis has the same issues as the plot above. Much overplotting (see all of the blue dots in 4b? those are all clustered into the upper left of 4a) and failure to show the variance explained by the PCs.Do you honestly not understand how much overplotting matters for attempting to understand these graphics? If not, here are some useful links:
https://www.data-to-viz.com/caveat/overplotting.html
https://www.jdatalab.com/data_science_and_data_mining/2017/01/26/overplotting-r.htmlI like the hexbin approach in the second link, but would need a variant which shows the groups as well as the number. Perhaps a variant where the bins are a colored pie chart? Hmm. I wonder if there is any package which does this. This looks close I wonder if it could be used to do this?
Another idea would be to use color saturation (rather than size) to show number of data points in a bin with hue in a pie chart to show the distribution.
https://homepages.thm.de/~admn12/pages/research/projectSomplot.htmlhttps://homepages.thm.de/~admn12/pages/research/somplot/oilsDemo.png1. Your effort towards coherence is appreciated. Please try to make it a way of life rather than something you do for a comment or two (or sometimes just part of one, like the one you linked) after I call you out about it. Regarding sincerity, I think the PCA examples above will make a useful case study in this regard. Remember your original assertion: "entirely clinal variation without any clustering." (I mention logical fallacies below, this is a great example of a false dichotomy)2. At least you admitted your initial approach was insincere. Any thoughts on when exactly that changed? IMO at best it is a process and is far from complete. Perhaps you could link to where you admitted being wrong about the "height stuff"? It would be helpful for me to see the specific details of that. As for my sincerity, I admit part of many of your primary points. Just in a more limited form. I think the way we each deal with (false) dichotomies and the reality in between should make quite clear which of us is being sincere. Some examples.
a. Gene flow exists. But it has not been sufficient to eliminate the group differences in genotype and phenotype between the continental races. It will impact how purely population genetics of humans follows a tree.
b. Population genetic clines exist (e.g. mixed race individuals). But the vast majority of populations group into genetic clusters.
c. Isolation by distance is important for genetic variation. But it is not the only relevant factor. Geographical and cultural barriers also matter. And IBD is not contra race--rather IBD is a partial cause of the races diverging.
Perhaps you can give similar examples for your perception of my viewpoints?3. Do you understand that you using the same arguments as all of the other anti-hereditarians is a big part of my problem with you? Many of those arguments are bad (e.g. based on logical fallacies). Hopefully some day you will figure that out. That many people say grass is purple does not make it so. Even when they conclusively prove it is not always green (e.g. when it dies it is brown, therefore grass is not always green, but that does not make it purple). And even when they shun or mob those who disagree with them:
https://www.unz.com/akarlin/persecution-of-iq-researchers/P.S. If you are sincere, why so coy about which "related field" you are in?
Blacks in Africa have a lot more genetic diversity than blacks in the US, whose ancestors overwhelmingly came from a small part of Africa where European slave traders could buy slaves and ship them across the ocean. And if you’re looking for a high-IQ population in Africa, check out the Igbo–I think they’re sometimes called the Jews of Africa.
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3644981 was one of my "coherent arguments" for example.I did that in the last thread but you never responded. Still, fair point so I will do so here.
You asked me a while back to show you a PCA that when sampling enough populations shows clines instead of races or clusters.Among another publication from a lab I cited earlier, I think this paper is interesting to show this. See for example the PCAs presented in the figures (particularly figure 4a) and the following text segments:The 1KGP sampled individuals from relatively distinct 110 population groups across the world, which makes the data particularly easy to cluster. Most medical cohorts comprise larger numbers of individuals sampled across extended geographical areas...We have scaled these three proportions to values between 120 and 255, to color individual points by their estimated admixture represented by RGB where red, green, and blue respectively correspond to African, European, and Asian/Native American ancestry. Using the first 10 principal components and UMAP, we demonstrate projections that present a collection of sub-populations and a continuum of genetic variation.
1. I will try to make them more coherent. They are sincere, I told you before if you quantitatively disprove them I have no issue changing my mind about something. 2. I am. are you? I was not initially true, but when I hear interesting arguments I stick around. I obviously disagree with most of the stuff you believe about race and IQ etc, but will reconsider something if shown to be wrong (like I did with the height stuff, Basal Eurasians being an African population and the paper about recent East Asian-Europe gene flow)3. That is up to you to decide. You will however, hear the same or similar arguments from every other person on the anti-hereditarian side you engage with about race. All the papers and links I have cited are peer-reviewed evidence and arguments used by experts in the field.
You say this after I have spent how many (hundreds?) comments trying to do just that?! How am I supposed to see you as sincere when you use dishonest rhetoric like that?
That was one of your better comments. The problem was it came 860 comments into a thread with 137 comments from you.
Regarding your point 3 there. I did show you such a tree in another thread.
https://www.unz.com/isteve/guardian-i-read-angela-sainis-superior-and-the-scales-fell-from-my-eyes/#comment-3643398
When you keep saying the same thing over and over again do you really expect me to respond to each and every comment saying the same thing?
Regarding your point 2: “You asked me to find you PCAs that are entirely clinal with no gaps. These PCAs support my argument of entirely clinal variation without any clustering. I did so.https://macarthurlab.org/2019/10/16/gnomad-v3-0/”
Let me give a sample of how I would like to see YOU engage. Here is the PCA in question (see how easy it is to include a picture or quote so we can have a concrete discussion without chasing links?):

That PCA is a mass of overplotting which I believe overstates the importance of the clines relative to the clusters. Keep in mind that your assertion was entirely clinal variation without any clustering. You clearly see a few clusters there: Finns, Amish, and Ashkenazi Jewish. You also clearly see the structure as a triangle with the three vertices being East Asian, African, and European (BTW, one interesting thing is how little East Asian/African mixing there is).
So you see that your graphic actually does not show what you claimed. It does show some clinal variation. And I have agreed many times that mixed race people exist. But you can clearly see some of those clusters and a better plot showing density in those heavily overplotted areas would make the others more clear.
So I expend time, effort, and words to prove you wrong, but will you admit it? I know the answer already (experience is a good teacher), but let’s let it play out so others can see. Repeat this process manyfold and maybe you (and anyone else reading this who cares) will see why I am sick of dealing with you. Frankly, I don’t care what you think anymore. I just want to make sure no one else here is misled by your misinformation.
One weakness of that PCA plot is it fails to show the percent variance explained for the PCs. A notable feature of PCA plots like this (at least the better ones which include that critical information) is just how much of the genetic variance is explained by those two PCs. In particular PC1 corresponding to the European-African variation.
Here is Figure 4a. See how easy this is?

This has the same issues as the plot above. Much overplotting (see all of the blue dots in 4b? those are all clustered into the upper left of 4a) and failure to show the variance explained by the PCs.
Do you honestly not understand how much overplotting matters for attempting to understand these graphics? If not, here are some useful links:
https://www.data-to-viz.com/caveat/overplotting.html
https://www.jdatalab.com/data_science_and_data_mining/2017/01/26/overplotting-r.html
I like the hexbin approach in the second link, but would need a variant which shows the groups as well as the number. Perhaps a variant where the bins are a colored pie chart? Hmm. I wonder if there is any package which does this. This looks close I wonder if it could be used to do this?

Another idea would be to use color saturation (rather than size) to show number of data points in a bin with hue in a pie chart to show the distribution.
https://homepages.thm.de/~admn12/pages/research/projectSomplot.html
1. Your effort towards coherence is appreciated. Please try to make it a way of life rather than something you do for a comment or two (or sometimes just part of one, like the one you linked) after I call you out about it. Regarding sincerity, I think the PCA examples above will make a useful case study in this regard. Remember your original assertion: “entirely clinal variation without any clustering.” (I mention logical fallacies below, this is a great example of a false dichotomy)
2. At least you admitted your initial approach was insincere. Any thoughts on when exactly that changed? IMO at best it is a process and is far from complete. Perhaps you could link to where you admitted being wrong about the “height stuff”? It would be helpful for me to see the specific details of that. As for my sincerity, I admit part of many of your primary points. Just in a more limited form. I think the way we each deal with (false) dichotomies and the reality in between should make quite clear which of us is being sincere. Some examples.
a. Gene flow exists. But it has not been sufficient to eliminate the group differences in genotype and phenotype between the continental races. It will impact how purely population genetics of humans follows a tree.
b. Population genetic clines exist (e.g. mixed race individuals). But the vast majority of populations group into genetic clusters.
c. Isolation by distance is important for genetic variation. But it is not the only relevant factor. Geographical and cultural barriers also matter. And IBD is not contra race–rather IBD is a partial cause of the races diverging.
Perhaps you can give similar examples for your perception of my viewpoints?
3. Do you understand that you using the same arguments as all of the other anti-hereditarians is a big part of my problem with you? Many of those arguments are bad (e.g. based on logical fallacies). Hopefully some day you will figure that out. That many people say grass is purple does not make it so. Even when they conclusively prove it is not always green (e.g. when it dies it is brown, therefore grass is not always green, but that does not make it purple). And even when they shun or mob those who disagree with them:
https://www.unz.com/akarlin/persecution-of-iq-researchers/
P.S. If you are sincere, why so coy about which “related field” you are in?
https://macarthurlab.org/2019/10/16/gnomad-v3-0/
Some notes.
- The colored ancestry classifications are based on the first 10 PCs. Not just the first two shown in the graphic. That is how they resolve between Finns, Amish, and Ashkenazi Jews in the lower right "European" corner. Remember, PCA is not just about the first two PCs commonly graphed. It's just that that is the most convenient representation to show. The higher order PCs are often useful for resolving finer population structure while the PC2 vs. PC1 plot does a good job of showing variation between African, East Asian, and European ancestry. Here is their description of the ancestry assignment process:- Near the beginning of the page they give sample numbers for each group. This helps give a quantitative idea of how much overplotting there is. There are 71,702 dots total. 5,244 of those are the Finns in that little blue grouping at the lower right. 32,299 of those are light blue non-Finnish Europeans (notice my comment about Figure 4b above). So it looks like over half the sample is in that mostly European V at the lower right. Two populations which are well known to be heavily admixed (African-Americans and Latinos) make up most of the clines you see. Notice how the 6,835 red Latino points take up so much more space visually than the Europeans. That's overplotting in action. Hopefully even you can see and acknowledge that.
Here is the full table, but probably better to use the formatted version at the link.
Anyways, it is physical anthropology with a focus on evolutionary anthropology.
You think I am being insincere where in fact I am just applying the knowledge I have of the subject to the debate. Theodore for example, says gene flow would be irrelevant but every single paper and book I have read on phylogenetics and race argues the opposite. So when I stress it, it is not out of insincerity but rather because it is relevant and many here just hand wave it away.Right, but genotypically humans are very closely related. Ask a geneticist if you do not believe me. There are variations in phenotype, sometimes corresponding to "race" but that is not particularly informative of variations in genotype, rather it is mostly due to shared geographic ancestry. What I mean is that black people for example share a similar phenotype but are a paraphyletic group, with some African populations being closer to Eurasians than other African populations. If humans do not form a tree, then race is not informative of evolutionary relationships though. It is what systematics is all about. You will think I am being insincere again, but please open a systematics text or even a paper (for example about subspecies: https://academic.oup.com/sysbio/article-abstract/2/3/97/1674750?redirectedFrom=fulltext)
(I could not copy/paste from it the relevant excerpts unfortunately).But how do we find these genetic clusters? There are user dependent and there is no right answer to the number of K.
Is there any objective way of determining K? (Genuine question here, I really do not know. Recently however, Graham Coop released an updated version of his Popgen notes, and he states the same as I did)
Did you read the Lawson et al, 2018 paper?Ok, fair enough here. Though there is a way to test that. See this tweet for example which I had saved but forgot to link: https://twitter.com/itsbirdemic/status/1137021740373204992So if you are interested in continuing this discussion, what we can do is look at those intermediate populations and their allele frequencies. I think it is an objective way to test both Templeton's model of human evolution and the degree to which IBD explains the patterns of genetic variation in humans.Sure.
1. Human populations differ and there are biological correlates to our idea of race. If one defines race strictly by phenotype then the concept is most likely applicable to some extent.
2. There has been relatively little gene flow between Africa and Southeast Asia for example, and most likely none between the Americas and the Old world prior to the European colonization.
3. there are population differences in height, BMI and some medically-relevant traits. Generally, for traits of which we have evidence of directional selection and show high between population differentiation, differences correlate to some extent with ancestral populations or what you would call race.No, on the contrary, in topics where I do not know much (for example advanced genomics) going by expert consensus seems the reasonable thing to do.
https://www.unz.com/isteve/guardian-i-read-angela-sainis-superior-and-the-scales-fell-from-my-eyes/#comment-3643398
When you keep saying the same thing over and over again do you really expect me to respond to each and every comment saying the same thing?Regarding your point 2: "You asked me to find you PCAs that are entirely clinal with no gaps. These PCAs support my argument of entirely clinal variation without any clustering. I did so.https://macarthurlab.org/2019/10/16/gnomad-v3-0/"Let me give a sample of how I would like to see YOU engage. Here is the PCA in question (see how easy it is to include a picture or quote so we can have a concrete discussion without chasing links?):https://macarthurlab.files.wordpress.com/2019/10/ancestry_pca.pngThat PCA is a mass of overplotting which I believe overstates the importance of the clines relative to the clusters. Keep in mind that your assertion was entirely clinal variation without any clustering. You clearly see a few clusters there: Finns, Amish, and Ashkenazi Jewish. You also clearly see the structure as a triangle with the three vertices being East Asian, African, and European (BTW, one interesting thing is how little East Asian/African mixing there is).So you see that your graphic actually does not show what you claimed. It does show some clinal variation. And I have agreed many times that mixed race people exist. But you can clearly see some of those clusters and a better plot showing density in those heavily overplotted areas would make the others more clear.So I expend time, effort, and words to prove you wrong, but will you admit it? I know the answer already (experience is a good teacher), but let's let it play out so others can see. Repeat this process manyfold and maybe you (and anyone else reading this who cares) will see why I am sick of dealing with you. Frankly, I don't care what you think anymore. I just want to make sure no one else here is misled by your misinformation.One weakness of that PCA plot is it fails to show the percent variance explained for the PCs. A notable feature of PCA plots like this (at least the better ones which include that critical information) is just how much of the genetic variance is explained by those two PCs. In particular PC1 corresponding to the European-African variation.Here is Figure 4a. See how easy this is?https://www.biorxiv.org/content/biorxiv/early/2019/03/16/423632/F4.large.jpgThis has the same issues as the plot above. Much overplotting (see all of the blue dots in 4b? those are all clustered into the upper left of 4a) and failure to show the variance explained by the PCs.Do you honestly not understand how much overplotting matters for attempting to understand these graphics? If not, here are some useful links:
https://www.data-to-viz.com/caveat/overplotting.html
https://www.jdatalab.com/data_science_and_data_mining/2017/01/26/overplotting-r.htmlI like the hexbin approach in the second link, but would need a variant which shows the groups as well as the number. Perhaps a variant where the bins are a colored pie chart? Hmm. I wonder if there is any package which does this. This looks close I wonder if it could be used to do this?
Another idea would be to use color saturation (rather than size) to show number of data points in a bin with hue in a pie chart to show the distribution.
https://homepages.thm.de/~admn12/pages/research/projectSomplot.htmlhttps://homepages.thm.de/~admn12/pages/research/somplot/oilsDemo.png1. Your effort towards coherence is appreciated. Please try to make it a way of life rather than something you do for a comment or two (or sometimes just part of one, like the one you linked) after I call you out about it. Regarding sincerity, I think the PCA examples above will make a useful case study in this regard. Remember your original assertion: "entirely clinal variation without any clustering." (I mention logical fallacies below, this is a great example of a false dichotomy)2. At least you admitted your initial approach was insincere. Any thoughts on when exactly that changed? IMO at best it is a process and is far from complete. Perhaps you could link to where you admitted being wrong about the "height stuff"? It would be helpful for me to see the specific details of that. As for my sincerity, I admit part of many of your primary points. Just in a more limited form. I think the way we each deal with (false) dichotomies and the reality in between should make quite clear which of us is being sincere. Some examples.
a. Gene flow exists. But it has not been sufficient to eliminate the group differences in genotype and phenotype between the continental races. It will impact how purely population genetics of humans follows a tree.
b. Population genetic clines exist (e.g. mixed race individuals). But the vast majority of populations group into genetic clusters.
c. Isolation by distance is important for genetic variation. But it is not the only relevant factor. Geographical and cultural barriers also matter. And IBD is not contra race--rather IBD is a partial cause of the races diverging.
Perhaps you can give similar examples for your perception of my viewpoints?3. Do you understand that you using the same arguments as all of the other anti-hereditarians is a big part of my problem with you? Many of those arguments are bad (e.g. based on logical fallacies). Hopefully some day you will figure that out. That many people say grass is purple does not make it so. Even when they conclusively prove it is not always green (e.g. when it dies it is brown, therefore grass is not always green, but that does not make it purple). And even when they shun or mob those who disagree with them:
https://www.unz.com/akarlin/persecution-of-iq-researchers/P.S. If you are sincere, why so coy about which "related field" you are in?
I should give some more details about that PCA plot. First, I broke your gnomAD page link by attempting to put it in quotes. Here is a working version.
https://macarthurlab.org/2019/10/16/gnomad-v3-0/
Some notes.
– The colored ancestry classifications are based on the first 10 PCs. Not just the first two shown in the graphic. That is how they resolve between Finns, Amish, and Ashkenazi Jews in the lower right “European” corner. Remember, PCA is not just about the first two PCs commonly graphed. It’s just that that is the most convenient representation to show. The higher order PCs are often useful for resolving finer population structure while the PC2 vs. PC1 plot does a good job of showing variation between African, East Asian, and European ancestry. Here is their description of the ancestry assignment process:
– Near the beginning of the page they give sample numbers for each group. This helps give a quantitative idea of how much overplotting there is. There are 71,702 dots total. 5,244 of those are the Finns in that little blue grouping at the lower right. 32,299 of those are light blue non-Finnish Europeans (notice my comment about Figure 4b above). So it looks like over half the sample is in that mostly European V at the lower right. Two populations which are well known to be heavily admixed (African-Americans and Latinos) make up most of the clines you see. Notice how the 6,835 red Latino points take up so much more space visually than the Europeans. That’s overplotting in action. Hopefully even you can see and acknowledge that.
Here is the full table, but probably better to use the formatted version at the link.
https://www.unz.com/isteve/guardian-i-read-angela-sainis-superior-and-the-scales-fell-from-my-eyes/#comment-3643398
When you keep saying the same thing over and over again do you really expect me to respond to each and every comment saying the same thing?Regarding your point 2: "You asked me to find you PCAs that are entirely clinal with no gaps. These PCAs support my argument of entirely clinal variation without any clustering. I did so.https://macarthurlab.org/2019/10/16/gnomad-v3-0/"Let me give a sample of how I would like to see YOU engage. Here is the PCA in question (see how easy it is to include a picture or quote so we can have a concrete discussion without chasing links?):https://macarthurlab.files.wordpress.com/2019/10/ancestry_pca.pngThat PCA is a mass of overplotting which I believe overstates the importance of the clines relative to the clusters. Keep in mind that your assertion was entirely clinal variation without any clustering. You clearly see a few clusters there: Finns, Amish, and Ashkenazi Jewish. You also clearly see the structure as a triangle with the three vertices being East Asian, African, and European (BTW, one interesting thing is how little East Asian/African mixing there is).So you see that your graphic actually does not show what you claimed. It does show some clinal variation. And I have agreed many times that mixed race people exist. But you can clearly see some of those clusters and a better plot showing density in those heavily overplotted areas would make the others more clear.So I expend time, effort, and words to prove you wrong, but will you admit it? I know the answer already (experience is a good teacher), but let's let it play out so others can see. Repeat this process manyfold and maybe you (and anyone else reading this who cares) will see why I am sick of dealing with you. Frankly, I don't care what you think anymore. I just want to make sure no one else here is misled by your misinformation.One weakness of that PCA plot is it fails to show the percent variance explained for the PCs. A notable feature of PCA plots like this (at least the better ones which include that critical information) is just how much of the genetic variance is explained by those two PCs. In particular PC1 corresponding to the European-African variation.Here is Figure 4a. See how easy this is?https://www.biorxiv.org/content/biorxiv/early/2019/03/16/423632/F4.large.jpgThis has the same issues as the plot above. Much overplotting (see all of the blue dots in 4b? those are all clustered into the upper left of 4a) and failure to show the variance explained by the PCs.Do you honestly not understand how much overplotting matters for attempting to understand these graphics? If not, here are some useful links:
https://www.data-to-viz.com/caveat/overplotting.html
https://www.jdatalab.com/data_science_and_data_mining/2017/01/26/overplotting-r.htmlI like the hexbin approach in the second link, but would need a variant which shows the groups as well as the number. Perhaps a variant where the bins are a colored pie chart? Hmm. I wonder if there is any package which does this. This looks close I wonder if it could be used to do this?
Another idea would be to use color saturation (rather than size) to show number of data points in a bin with hue in a pie chart to show the distribution.
https://homepages.thm.de/~admn12/pages/research/projectSomplot.htmlhttps://homepages.thm.de/~admn12/pages/research/somplot/oilsDemo.png1. Your effort towards coherence is appreciated. Please try to make it a way of life rather than something you do for a comment or two (or sometimes just part of one, like the one you linked) after I call you out about it. Regarding sincerity, I think the PCA examples above will make a useful case study in this regard. Remember your original assertion: "entirely clinal variation without any clustering." (I mention logical fallacies below, this is a great example of a false dichotomy)2. At least you admitted your initial approach was insincere. Any thoughts on when exactly that changed? IMO at best it is a process and is far from complete. Perhaps you could link to where you admitted being wrong about the "height stuff"? It would be helpful for me to see the specific details of that. As for my sincerity, I admit part of many of your primary points. Just in a more limited form. I think the way we each deal with (false) dichotomies and the reality in between should make quite clear which of us is being sincere. Some examples.
a. Gene flow exists. But it has not been sufficient to eliminate the group differences in genotype and phenotype between the continental races. It will impact how purely population genetics of humans follows a tree.
b. Population genetic clines exist (e.g. mixed race individuals). But the vast majority of populations group into genetic clusters.
c. Isolation by distance is important for genetic variation. But it is not the only relevant factor. Geographical and cultural barriers also matter. And IBD is not contra race--rather IBD is a partial cause of the races diverging.
Perhaps you can give similar examples for your perception of my viewpoints?3. Do you understand that you using the same arguments as all of the other anti-hereditarians is a big part of my problem with you? Many of those arguments are bad (e.g. based on logical fallacies). Hopefully some day you will figure that out. That many people say grass is purple does not make it so. Even when they conclusively prove it is not always green (e.g. when it dies it is brown, therefore grass is not always green, but that does not make it purple). And even when they shun or mob those who disagree with them:
https://www.unz.com/akarlin/persecution-of-iq-researchers/P.S. If you are sincere, why so coy about which "related field" you are in?
Will reply to the rest of your post later, but if you saw my last post on that Thompson thread (or one of the last ones) you would see I answered your question about my field.
Anyways, it is physical anthropology with a focus on evolutionary anthropology.
Some of the literature in your field is entertaining:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299519/This one looks like it has decent correspondence with your views (would you agree?):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6075721/But can one really take seriously an assertion like this?The level of intellectual effort devoted to pretending race does not have a biological basis is truly impressive (if more than a bit wasteful and depressing IMO).
P.S. For context (for others, not you obviously) this is worth a look:
https://www.oxfordbibliographies.com/view/document/obo-9780199766567/obo-9780199766567-0054.xml
Anyways, it is physical anthropology with a focus on evolutionary anthropology.
Thanks. That is interesting because physical (aka biological) anthropology tends to be the science based side of the field. My understanding is race is a major topic of controversy in anthropology which helps explain both your interest in the topic and your position.
Some of the literature in your field is entertaining:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299519/
This one looks like it has decent correspondence with your views (would you agree?):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6075721/
But can one really take seriously an assertion like this?
The level of intellectual effort devoted to pretending race does not have a biological basis is truly impressive (if more than a bit wasteful and depressing IMO).
P.S. For context (for others, not you obviously) this is worth a look:
https://www.oxfordbibliographies.com/view/document/obo-9780199766567/obo-9780199766567-0054.xml
And I should briefly say here, that when I say race is a social construct I do not mean it has no biological correlates (since you also replied to another post of mine).Believe it or not, I actually agree more with you here. In theory, if race is real it does not matter whether people in the past recognized it or not. So yes, this assertion is not particularly useful in the debate.Why wasteful and depressing? I also found it depressing when people on twitter were posting under scientists sharing Ewan Birney's et al. post on race with links to the Thompson or Sailer thread, trying to hand wave away all the literature and expert's opinion on the topic in order to (at least what it seemed to me) justify that racism is somehow acceptable because people with black skin have innately lower IQ.
Some of the literature in your field is entertaining:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299519/This one looks like it has decent correspondence with your views (would you agree?):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6075721/But can one really take seriously an assertion like this?The level of intellectual effort devoted to pretending race does not have a biological basis is truly impressive (if more than a bit wasteful and depressing IMO).
P.S. For context (for others, not you obviously) this is worth a look:
https://www.oxfordbibliographies.com/view/document/obo-9780199766567/obo-9780199766567-0054.xml
Yes, though there is a broad consensus it does not apply to humans.
Yes, it does indeed closely align with my views.
And I should briefly say here, that when I say race is a social construct I do not mean it has no biological correlates (since you also replied to another post of mine).
Believe it or not, I actually agree more with you here. In theory, if race is real it does not matter whether people in the past recognized it or not. So yes, this assertion is not particularly useful in the debate.
Why wasteful and depressing?
I also found it depressing when people on twitter were posting under scientists sharing Ewan Birney’s et al. post on race with links to the Thompson or Sailer thread, trying to hand wave away all the literature and expert’s opinion on the topic in order to (at least what it seemed to me) justify that racism is somehow acceptable because people with black skin have innately lower IQ.
People through all time recognize the concepts of "us" and "them." That becomes even easier to recognize when there are physical differences. Which it seems obvious would influence perceptions of us and various "them"s.
I find the assertion that those biological correlates have no causal relationship to human perception of race to be dumbfounding.Let's include the whole sentence. (if you find yourself quoting fragments of a sentence it is a decent clue you have removed useful context and are quoting selectively)I would have hoped it would be obvious that I was referring to the "pretending" part. If I am right then that is a great deal of effort expended on something that is at best an error and at worst a lie. Sure sounds wasteful and depressing to me.Your "seemed to me" reads a great deal into people's intent. Might want to be more careful about that. Framing things in moral good vs. evil terms is a quick route to emotion rather than science based thinking.
Framed that way your example is morally depressing. My example is depressing from a scientific point of view.
I think I (and others) have responded to Birney et al.'s points enough in the relevant Unz Review threads. That you find his statements compelling baffles me. Frankly, I find Birney et al.'s assertions laughable. As is the fact that they are perceived as experts.
At this point I think anthropology is engaging in Lysenko levels of mistakeness as far as race goes. Letting politics drive science is a bad idea.
https://www.unz.com/isteve/guardian-i-read-angela-sainis-superior-and-the-scales-fell-from-my-eyes/#comment-3643398
When you keep saying the same thing over and over again do you really expect me to respond to each and every comment saying the same thing?Regarding your point 2: "You asked me to find you PCAs that are entirely clinal with no gaps. These PCAs support my argument of entirely clinal variation without any clustering. I did so.https://macarthurlab.org/2019/10/16/gnomad-v3-0/"Let me give a sample of how I would like to see YOU engage. Here is the PCA in question (see how easy it is to include a picture or quote so we can have a concrete discussion without chasing links?):https://macarthurlab.files.wordpress.com/2019/10/ancestry_pca.pngThat PCA is a mass of overplotting which I believe overstates the importance of the clines relative to the clusters. Keep in mind that your assertion was entirely clinal variation without any clustering. You clearly see a few clusters there: Finns, Amish, and Ashkenazi Jewish. You also clearly see the structure as a triangle with the three vertices being East Asian, African, and European (BTW, one interesting thing is how little East Asian/African mixing there is).So you see that your graphic actually does not show what you claimed. It does show some clinal variation. And I have agreed many times that mixed race people exist. But you can clearly see some of those clusters and a better plot showing density in those heavily overplotted areas would make the others more clear.So I expend time, effort, and words to prove you wrong, but will you admit it? I know the answer already (experience is a good teacher), but let's let it play out so others can see. Repeat this process manyfold and maybe you (and anyone else reading this who cares) will see why I am sick of dealing with you. Frankly, I don't care what you think anymore. I just want to make sure no one else here is misled by your misinformation.One weakness of that PCA plot is it fails to show the percent variance explained for the PCs. A notable feature of PCA plots like this (at least the better ones which include that critical information) is just how much of the genetic variance is explained by those two PCs. In particular PC1 corresponding to the European-African variation.Here is Figure 4a. See how easy this is?https://www.biorxiv.org/content/biorxiv/early/2019/03/16/423632/F4.large.jpgThis has the same issues as the plot above. Much overplotting (see all of the blue dots in 4b? those are all clustered into the upper left of 4a) and failure to show the variance explained by the PCs.Do you honestly not understand how much overplotting matters for attempting to understand these graphics? If not, here are some useful links:
https://www.data-to-viz.com/caveat/overplotting.html
https://www.jdatalab.com/data_science_and_data_mining/2017/01/26/overplotting-r.htmlI like the hexbin approach in the second link, but would need a variant which shows the groups as well as the number. Perhaps a variant where the bins are a colored pie chart? Hmm. I wonder if there is any package which does this. This looks close I wonder if it could be used to do this?
Another idea would be to use color saturation (rather than size) to show number of data points in a bin with hue in a pie chart to show the distribution.
https://homepages.thm.de/~admn12/pages/research/projectSomplot.htmlhttps://homepages.thm.de/~admn12/pages/research/somplot/oilsDemo.png1. Your effort towards coherence is appreciated. Please try to make it a way of life rather than something you do for a comment or two (or sometimes just part of one, like the one you linked) after I call you out about it. Regarding sincerity, I think the PCA examples above will make a useful case study in this regard. Remember your original assertion: "entirely clinal variation without any clustering." (I mention logical fallacies below, this is a great example of a false dichotomy)2. At least you admitted your initial approach was insincere. Any thoughts on when exactly that changed? IMO at best it is a process and is far from complete. Perhaps you could link to where you admitted being wrong about the "height stuff"? It would be helpful for me to see the specific details of that. As for my sincerity, I admit part of many of your primary points. Just in a more limited form. I think the way we each deal with (false) dichotomies and the reality in between should make quite clear which of us is being sincere. Some examples.
a. Gene flow exists. But it has not been sufficient to eliminate the group differences in genotype and phenotype between the continental races. It will impact how purely population genetics of humans follows a tree.
b. Population genetic clines exist (e.g. mixed race individuals). But the vast majority of populations group into genetic clusters.
c. Isolation by distance is important for genetic variation. But it is not the only relevant factor. Geographical and cultural barriers also matter. And IBD is not contra race--rather IBD is a partial cause of the races diverging.
Perhaps you can give similar examples for your perception of my viewpoints?3. Do you understand that you using the same arguments as all of the other anti-hereditarians is a big part of my problem with you? Many of those arguments are bad (e.g. based on logical fallacies). Hopefully some day you will figure that out. That many people say grass is purple does not make it so. Even when they conclusively prove it is not always green (e.g. when it dies it is brown, therefore grass is not always green, but that does not make it purple). And even when they shun or mob those who disagree with them:
https://www.unz.com/akarlin/persecution-of-iq-researchers/P.S. If you are sincere, why so coy about which "related field" you are in?
I still have not had time to go through all your links so I am replying to only the latter segment of your reply.
I admitted before I did not initially argue in good faith. Since you seem to be doing that now, I will do my best to reciprocate. You have to understand though, most of the people I have debated on this usually use it only as a way to justify their ideology , more often that not including plans to separate people of color from white people or other racist policies which I am strongly opposed to.
If the dots where not painted or if sampling had been even more representative, would you be able to tell? But I am hesitant to strongly assert that point as I have not yet gone through your links.
I do not remember when I admitted that you were right about the height stuff, in any case, if I did not do so earlier then I do so now.
You think I am being insincere where in fact I am just applying the knowledge I have of the subject to the debate. Theodore for example, says gene flow would be irrelevant but every single paper and book I have read on phylogenetics and race argues the opposite. So when I stress it, it is not out of insincerity but rather because it is relevant and many here just hand wave it away.
Right, but genotypically humans are very closely related. Ask a geneticist if you do not believe me. There are variations in phenotype, sometimes corresponding to “race” but that is not particularly informative of variations in genotype, rather it is mostly due to shared geographic ancestry.
What I mean is that black people for example share a similar phenotype but are a paraphyletic group, with some African populations being closer to Eurasians than other African populations.
If humans do not form a tree, then race is not informative of evolutionary relationships though. It is what systematics is all about. You will think I am being insincere again, but please open a systematics text or even a paper (for example about subspecies: https://academic.oup.com/sysbio/article-abstract/2/3/97/1674750?redirectedFrom=fulltext)
(I could not copy/paste from it the relevant excerpts unfortunately).
But how do we find these genetic clusters? There are user dependent and there is no right answer to the number of K.
Is there any objective way of determining K? (Genuine question here, I really do not know. Recently however, Graham Coop released an updated version of his Popgen notes, and he states the same as I did)
Did you read the Lawson et al, 2018 paper?
Ok, fair enough here. Though there is a way to test that. See this tweet for example which I had saved but forgot to link: https://twitter.com/itsbirdemic/status/1137021740373204992
So if you are interested in continuing this discussion, what we can do is look at those intermediate populations and their allele frequencies. I think it is an objective way to test both Templeton’s model of human evolution and the degree to which IBD explains the patterns of genetic variation in humans.
Sure.
1. Human populations differ and there are biological correlates to our idea of race. If one defines race strictly by phenotype then the concept is most likely applicable to some extent.
2. There has been relatively little gene flow between Africa and Southeast Asia for example, and most likely none between the Americas and the Old world prior to the European colonization.
3. there are population differences in height, BMI and some medically-relevant traits. Generally, for traits of which we have evidence of directional selection and show high between population differentiation, differences correlate to some extent with ancestral populations or what you would call race.
No, on the contrary, in topics where I do not know much (for example advanced genomics) going by expert consensus seems the reasonable thing to do.
italics - As far as I am concerned that and race are a distinction without a difference.Examples? And don't play games with North Africans who clearly group separately from sub-Saharan Africans.The question is to what degree is a tree representation accurate. Please stop with the false dichotomies. Either you are an extremely sloppy thinker or think I am.
We have very different ideas of which references and arguments we find credible.We can look visually at the clustering to get some idea. Beyond that, yes there are methods, but as you note they are imperfect. Which is not at all the same as useless or meaningless (more false dichotomies, don't let the perfect be the enemy of the good).There are objective methods, but cherry picking between them can allow subjectivity to creep in. See the "Determining Optimal Number of Clusters" at https://towardsdatascience.com/10-tips-for-choosing-the-optimal-number-of-clusters-277e93d72d92Link papers if you want me to respond.Did you happen to notice that Bird included no evidence for his position? Evidence matters.1. Phenotype is related to genotype.
2. So do those splits with little gene flow work as demarcations for groups?
3. And skin color. And hair type. And pygmy height... Yet somehow this correlation is not enough to make "what you would call race" a usable construct. Interesting.It is. Except when the experts quite consistently ignore provocative points (e.g. Graham Coop, you might try reading between the lines of what he says and doesn't say a bit more, what I like about him is he seems to stick to the truth) or else actively lie and misrepresent (e.g. Ewan Birney and Kevin Bird) IMO.
And I should briefly say here, that when I say race is a social construct I do not mean it has no biological correlates (since you also replied to another post of mine).Believe it or not, I actually agree more with you here. In theory, if race is real it does not matter whether people in the past recognized it or not. So yes, this assertion is not particularly useful in the debate.Why wasteful and depressing? I also found it depressing when people on twitter were posting under scientists sharing Ewan Birney's et al. post on race with links to the Thompson or Sailer thread, trying to hand wave away all the literature and expert's opinion on the topic in order to (at least what it seemed to me) justify that racism is somehow acceptable because people with black skin have innately lower IQ.
But by that you seem to be implying that those biological correlates had no influence on the way humans perceive race. Is that an accurate reflection of your views?
People through all time recognize the concepts of “us” and “them.” That becomes even easier to recognize when there are physical differences. Which it seems obvious would influence perceptions of us and various “them”s.
I find the assertion that those biological correlates have no causal relationship to human perception of race to be dumbfounding.
Let’s include the whole sentence. (if you find yourself quoting fragments of a sentence it is a decent clue you have removed useful context and are quoting selectively)
I would have hoped it would be obvious that I was referring to the “pretending” part. If I am right then that is a great deal of effort expended on something that is at best an error and at worst a lie. Sure sounds wasteful and depressing to me.
Your “seemed to me” reads a great deal into people’s intent. Might want to be more careful about that. Framing things in moral good vs. evil terms is a quick route to emotion rather than science based thinking.
Framed that way your example is morally depressing. My example is depressing from a scientific point of view.
I think I (and others) have responded to Birney et al.’s points enough in the relevant Unz Review threads. That you find his statements compelling baffles me. Frankly, I find Birney et al.’s assertions laughable. As is the fact that they are perceived as experts.
At this point I think anthropology is engaging in Lysenko levels of mistakeness as far as race goes. Letting politics drive science is a bad idea.
I am not a communist btw, in case you are wondering.Do you honestly believe this does not happen with many HBD people? Why does race realist and anti immigration views go hand in hand then?
You think I am being insincere where in fact I am just applying the knowledge I have of the subject to the debate. Theodore for example, says gene flow would be irrelevant but every single paper and book I have read on phylogenetics and race argues the opposite. So when I stress it, it is not out of insincerity but rather because it is relevant and many here just hand wave it away.Right, but genotypically humans are very closely related. Ask a geneticist if you do not believe me. There are variations in phenotype, sometimes corresponding to "race" but that is not particularly informative of variations in genotype, rather it is mostly due to shared geographic ancestry. What I mean is that black people for example share a similar phenotype but are a paraphyletic group, with some African populations being closer to Eurasians than other African populations. If humans do not form a tree, then race is not informative of evolutionary relationships though. It is what systematics is all about. You will think I am being insincere again, but please open a systematics text or even a paper (for example about subspecies: https://academic.oup.com/sysbio/article-abstract/2/3/97/1674750?redirectedFrom=fulltext)
(I could not copy/paste from it the relevant excerpts unfortunately).But how do we find these genetic clusters? There are user dependent and there is no right answer to the number of K.
Is there any objective way of determining K? (Genuine question here, I really do not know. Recently however, Graham Coop released an updated version of his Popgen notes, and he states the same as I did)
Did you read the Lawson et al, 2018 paper?Ok, fair enough here. Though there is a way to test that. See this tweet for example which I had saved but forgot to link: https://twitter.com/itsbirdemic/status/1137021740373204992So if you are interested in continuing this discussion, what we can do is look at those intermediate populations and their allele frequencies. I think it is an objective way to test both Templeton's model of human evolution and the degree to which IBD explains the patterns of genetic variation in humans.Sure.
1. Human populations differ and there are biological correlates to our idea of race. If one defines race strictly by phenotype then the concept is most likely applicable to some extent.
2. There has been relatively little gene flow between Africa and Southeast Asia for example, and most likely none between the Americas and the Old world prior to the European colonization.
3. there are population differences in height, BMI and some medically-relevant traits. Generally, for traits of which we have evidence of directional selection and show high between population differentiation, differences correlate to some extent with ancestral populations or what you would call race.No, on the contrary, in topics where I do not know much (for example advanced genomics) going by expert consensus seems the reasonable thing to do.
And yet, population geneticists will report things like: self-identified African Americans are 82.1% sub-Saharan, 16.1% European, and 1.2% Native American.
Funny how that works …
But have you asked these geneticists their opinion on race?
Is European a useful category though? Is it really valid to group Greeks and Germans together to the exclusion of say, Palestinians?
Thanks for replying.
But have you asked these geneticists their opinion on race?
Is European a useful category though? Is it really valid to group Greeks and Germans together to the exclusion of say, Palestinians?
People through all time recognize the concepts of "us" and "them." That becomes even easier to recognize when there are physical differences. Which it seems obvious would influence perceptions of us and various "them"s.
I find the assertion that those biological correlates have no causal relationship to human perception of race to be dumbfounding.Let's include the whole sentence. (if you find yourself quoting fragments of a sentence it is a decent clue you have removed useful context and are quoting selectively)I would have hoped it would be obvious that I was referring to the "pretending" part. If I am right then that is a great deal of effort expended on something that is at best an error and at worst a lie. Sure sounds wasteful and depressing to me.Your "seemed to me" reads a great deal into people's intent. Might want to be more careful about that. Framing things in moral good vs. evil terms is a quick route to emotion rather than science based thinking.
Framed that way your example is morally depressing. My example is depressing from a scientific point of view.
I think I (and others) have responded to Birney et al.'s points enough in the relevant Unz Review threads. That you find his statements compelling baffles me. Frankly, I find Birney et al.'s assertions laughable. As is the fact that they are perceived as experts.
At this point I think anthropology is engaging in Lysenko levels of mistakeness as far as race goes. Letting politics drive science is a bad idea.
No, I did not mean that. Of course they influence they way that people perceive race.
I do not believe that.
I know what it was you were referring to. I just do not agree that they are pretending.
Not really, just a quick look at their timelines or subsequent arguments usually showed most of them espouse white nationalist or at the very least far right opinions and views. Is that not politics intruding into science?
Fair enough, this is why I am engaging with you on the topic. More so about the science not the moral aspect of the issue. I agree science is more important but wanted to give you some background as to why I initiated these discussions in case you were wondering about it.
I only referenced them here because of how I came across these posts on unz.com
You don’t have to answer of course, but have you discussed this with actual experts? Any geneticists or biologists (since I guess you do not hold my field in any high regard)
Most of the papers I have cited are from geneticists not anthropologists. Arguing that we engage in Lysenko levels of mistakeness as far as race goes would mean that for the last 50 years most of the people who engaged with the topic were all Lysenkoists. Hard to believe.
I am not a communist btw, in case you are wondering.
Do you honestly believe this does not happen with many HBD people? Why does race realist and anti immigration views go hand in hand then?
I went back and found your comment admitting being wrong about height (it wasn't that hard to search your comment history for it, maybe next time you could do the work yourself?):
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3627100I would be interested in knowing which particular piece(s) of evidence you found convincing for height. Because I think the evidence for IQ is about as convincing (not quite as good as Pygmy height though) as long as you recognize that no one "respectable" is going to publish on genetic causes of group differences in IQ.
On to your current comment.
Thank you for clarifying (somewhat) your take on the relationship of biological correlates to race. Rather than making me play guessing games about what you think, perhaps you could describe your position in more detail?
A brief summary of my position: I think race is a social construct overlaid on a biological reality. How well those two correlate varies greatly depending on circumstances. In particular, how much the base races differ and how much admixture there is in the groups in questions. Comparing unmixed Africans, East Asians, and Europeans we clearly see the importance of biology. For groups like Hispanics and heavily admixed African Americans the social construct aspect becomes more important.I'm not sure which is worse. Them pretending or them actually believing some of the things they say. I suspect the reality is a combination of pretense and ignorance. The balance varying by individual.Actual examples rather than just vague accusations would be helpful. Otherwise it just looks like a strawman. A decent rule of thumb would be to confine your arguments to the statements of the people you are actually arguing with when possible.Like whom? In public? Perhaps you are aware of a Nobel Prize winner named James Watson who talked honestly about racial differences? And what happened to him.Indeed. And a terrible indictment of their "science" if true.It happens to some degree with everyone. We are all biased. How well we manage to keep an open mind and work through that is what is important.
Do you have any examples of HBD people doing this in categorical way? Say comparable to people asserting that race is SOLELY a social construct?
The problem I am describing is real. Do you sincerely disagree this is happening? Here is a thoughtful look at the issue. Do you think Cofnas is on target?
Research on group differences in intelligence: A defense of free inquiry
https://www.tandfonline.com/doi/full/10.1080/09515089.2019.1697803
Abstract:Back to you.Because if you understand the science (or just have functioning eyes and intellect) it is clear that immigrants differ in their ability to blend in and contribute to our society. This has both cultural and biological aspects.
The way I see it the causality goes like this:
Eyes and genetics -> Recognize groups are different
Recognize groups are different -> race realist
Recognize groups are different -> desire to be more selective about immigration
I am not a communist btw, in case you are wondering.Do you honestly believe this does not happen with many HBD people? Why does race realist and anti immigration views go hand in hand then?
First, are you still planning on responding to my PCA points at some time? Because that seems like a clear case of me demonstrating you being wrong using a graphic of your own choosing.
I went back and found your comment admitting being wrong about height (it wasn’t that hard to search your comment history for it, maybe next time you could do the work yourself?):
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3627100
I would be interested in knowing which particular piece(s) of evidence you found convincing for height. Because I think the evidence for IQ is about as convincing (not quite as good as Pygmy height though) as long as you recognize that no one “respectable” is going to publish on genetic causes of group differences in IQ.
On to your current comment.
Thank you for clarifying (somewhat) your take on the relationship of biological correlates to race. Rather than making me play guessing games about what you think, perhaps you could describe your position in more detail?
A brief summary of my position: I think race is a social construct overlaid on a biological reality. How well those two correlate varies greatly depending on circumstances. In particular, how much the base races differ and how much admixture there is in the groups in questions. Comparing unmixed Africans, East Asians, and Europeans we clearly see the importance of biology. For groups like Hispanics and heavily admixed African Americans the social construct aspect becomes more important.
I’m not sure which is worse. Them pretending or them actually believing some of the things they say. I suspect the reality is a combination of pretense and ignorance. The balance varying by individual.
Actual examples rather than just vague accusations would be helpful. Otherwise it just looks like a strawman. A decent rule of thumb would be to confine your arguments to the statements of the people you are actually arguing with when possible.
Like whom? In public? Perhaps you are aware of a Nobel Prize winner named James Watson who talked honestly about racial differences? And what happened to him.
Indeed. And a terrible indictment of their “science” if true.
It happens to some degree with everyone. We are all biased. How well we manage to keep an open mind and work through that is what is important.
Do you have any examples of HBD people doing this in categorical way? Say comparable to people asserting that race is SOLELY a social construct?
The problem I am describing is real. Do you sincerely disagree this is happening? Here is a thoughtful look at the issue. Do you think Cofnas is on target?
Research on group differences in intelligence: A defense of free inquiry
https://www.tandfonline.com/doi/full/10.1080/09515089.2019.1697803
Abstract:
Back to you.
Because if you understand the science (or just have functioning eyes and intellect) it is clear that immigrants differ in their ability to blend in and contribute to our society. This has both cultural and biological aspects.
The way I see it the causality goes like this:
Eyes and genetics -> Recognize groups are different
Recognize groups are different -> race realist
Recognize groups are different -> desire to be more selective about immigration
https://www.pnas.org/content/111/35/E3596My position is that though they are biological correlates to race, race does not match the patterns of genetic diversity we see in worldwide human populations. Pretty much what these two tweets are saying: https://twitter.com/itsbirdemic/status/1222353680160215040
What would be your counter argument to that?res, my whole point is that there is no such thing as unmixed Africans, East Asians and Europeans.
Europeans for example are a mix of people closely related to modern-day Middle Easterners (which you guys think mixed rather than ancestral to Europeans) , local hunter-gatherers and Siberians from the north (Ancient North Eurasians).
Is your argument that these 3 populations were entirely West Eurasian or isolated from Africans or East Asians?
If indeed there are unmixed Europeans, Africans and East Asians (we can test that) or if ancient DNA shows different origins than I have presented above, then I am willing to admit races exist.Fine, forget the intermediate groups, lets focus on Europeans, Africans and East Asians as you say.Tell David Reich and Graham Coop that. Come on, you can not really believe they are just pretending or ignorant about the science.Fair enough, I am too I guess, but as you see willing to bypass any political motivations etc. I only brought it up because you did so before.Did he have evidence to back up his assertions? Did he put it in print? And actually, no, though I do not share his opinion I understand this is a politically charged topic and disagree with how he was treated. But don't forget, he has a history of making controversial statements and likes to provoke people. Ask geneticists who worked with him or know him. (So I have been told at least)Not you or Steve Sailer but @theodore and @mikemikev seemed to assert that. Asserting race=subspecies means it exists objectively and less so because of social construction (all taxonomy is constructed of course but that is a different story)Disagree that what is happening?Largely yes, though Reich did not assert what he claims he did. At least not any more after his newest papers.
Cofnas is saying these variants are likely to be found. Sure, but my point is they have not been found and are unlikely to, due to quantitative genetic models on human populations.(quick example for differential selection not being a good argument: https://twitter.com/ewanbirney/status/1221975246695063553
We can expand on that, but I do not want to gish-gallop this conversation. Also, I would appreciate if you could answer my comment #102.
I went back and found your comment admitting being wrong about height (it wasn't that hard to search your comment history for it, maybe next time you could do the work yourself?):
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3627100I would be interested in knowing which particular piece(s) of evidence you found convincing for height. Because I think the evidence for IQ is about as convincing (not quite as good as Pygmy height though) as long as you recognize that no one "respectable" is going to publish on genetic causes of group differences in IQ.
On to your current comment.
Thank you for clarifying (somewhat) your take on the relationship of biological correlates to race. Rather than making me play guessing games about what you think, perhaps you could describe your position in more detail?
A brief summary of my position: I think race is a social construct overlaid on a biological reality. How well those two correlate varies greatly depending on circumstances. In particular, how much the base races differ and how much admixture there is in the groups in questions. Comparing unmixed Africans, East Asians, and Europeans we clearly see the importance of biology. For groups like Hispanics and heavily admixed African Americans the social construct aspect becomes more important.I'm not sure which is worse. Them pretending or them actually believing some of the things they say. I suspect the reality is a combination of pretense and ignorance. The balance varying by individual.Actual examples rather than just vague accusations would be helpful. Otherwise it just looks like a strawman. A decent rule of thumb would be to confine your arguments to the statements of the people you are actually arguing with when possible.Like whom? In public? Perhaps you are aware of a Nobel Prize winner named James Watson who talked honestly about racial differences? And what happened to him.Indeed. And a terrible indictment of their "science" if true.It happens to some degree with everyone. We are all biased. How well we manage to keep an open mind and work through that is what is important.
Do you have any examples of HBD people doing this in categorical way? Say comparable to people asserting that race is SOLELY a social construct?
The problem I am describing is real. Do you sincerely disagree this is happening? Here is a thoughtful look at the issue. Do you think Cofnas is on target?
Research on group differences in intelligence: A defense of free inquiry
https://www.tandfonline.com/doi/full/10.1080/09515089.2019.1697803
Abstract:Back to you.Because if you understand the science (or just have functioning eyes and intellect) it is clear that immigrants differ in their ability to blend in and contribute to our society. This has both cultural and biological aspects.
The way I see it the causality goes like this:
Eyes and genetics -> Recognize groups are different
Recognize groups are different -> race realist
Recognize groups are different -> desire to be more selective about immigration
Yes soon, it does seem like you are correct, but need to read more about it. it looks like over plotting issues though, like you said.
well, since I said so in my earlier reply to you, I did not consider it important.
for example: https://www.biorxiv.org/content/10.1101/776377v1 and
https://www.pnas.org/content/111/35/E3596
My position is that though they are biological correlates to race, race does not match the patterns of genetic diversity we see in worldwide human populations. Pretty much what these two tweets are saying: https://twitter.com/itsbirdemic/status/1222353680160215040
What would be your counter argument to that?
res, my whole point is that there is no such thing as unmixed Africans, East Asians and Europeans.
Europeans for example are a mix of people closely related to modern-day Middle Easterners (which you guys think mixed rather than ancestral to Europeans) , local hunter-gatherers and Siberians from the north (Ancient North Eurasians).
Is your argument that these 3 populations were entirely West Eurasian or isolated from Africans or East Asians?
If indeed there are unmixed Europeans, Africans and East Asians (we can test that) or if ancient DNA shows different origins than I have presented above, then I am willing to admit races exist.
Fine, forget the intermediate groups, lets focus on Europeans, Africans and East Asians as you say.
Tell David Reich and Graham Coop that. Come on, you can not really believe they are just pretending or ignorant about the science.
Fair enough, I am too I guess, but as you see willing to bypass any political motivations etc. I only brought it up because you did so before.
Did he have evidence to back up his assertions? Did he put it in print? And actually, no, though I do not share his opinion I understand this is a politically charged topic and disagree with how he was treated. But don’t forget, he has a history of making controversial statements and likes to provoke people. Ask geneticists who worked with him or know him. (So I have been told at least)
Not you or Steve Sailer but @theodore and seemed to assert that. Asserting race=subspecies means it exists objectively and less so because of social construction (all taxonomy is constructed of course but that is a different story)
Disagree that what is happening?
Largely yes, though Reich did not assert what he claims he did. At least not any more after his newest papers.
Cofnas is saying these variants are likely to be found. Sure, but my point is they have not been found and are unlikely to, due to quantitative genetic models on human populations.(quick example for differential selection not being a good argument: https://twitter.com/ewanbirney/status/1221975246695063553
We can expand on that, but I do not want to gish-gallop this conversation. Also, I would appreciate if you could answer my comment #102.
I'll consider giving a counterargument if you provide something that contains an actual argument and/or evidence rather than a simple assertion. Do you not understand how pathetic it is to introduce tweets like that into an attempt to have a serious evidence based discussion?Fair enough. We are talking about two very different things.
1. How the different groups got to where they are today. Which is as you say a long chain of complex mixing.
2. Where the groups are today as shown by the clustering in the PCA plots.
When I talk about "unmixed" ... I am referring to individuals who clearly group into their respective clusters. As opposed to those who are mixed race (children of individuals of two different races). There is a third case--intermediate populations that form their own relatively stable intermediate groups. You focus on that third case all of the time, but the point of my PCA plot comments is that there are relatively few people like that compared to the numbers in the major clusters.
Do you deny that there are many people who clearly group into African, East Asian, and European clusters on PCA plots? Albeit obscured somewhat by overplotting in most plots we see.Thanks. That will help this conversation be more concrete and meaningful.Not them. They are two of the more truthful people I see out there. But both are very careful about what they do and do not say. And even given that, David Reich is walking a fine line.
And speaking of fine lines, it will be interesting to see if Kevin Bird gets cancelled over his recent paper showing African-European EDU PGS differences are partially genetic. You like citing him as a reference. Do you agree with him about that?
https://www.unz.com/isteve/the-mismeasure-of-genes/
When I say pretense I am often including the willful ignoring of controversial areas (with a subcategory of neither agreeing with nor criticizing people who repeat the party line, see Graham Coop's exchanges with people like Ewan Birney on Twitter). Which perhaps isn't strictly accurate, but IMHO close enough for most purposes.But you do agree that Watson is an object lesson in what can happen even to the most respected of scientists if he says something wrong about group differences, right? Given that, how can I (or you!) take anything a scientist says in public on these topics without a great deal of skepticism?When you find yourself asking questions like this please consider rereading the immediately preceding and following sentences. Here is more complete context: "The problem I am describing is real. Do you sincerely disagree this is happening? Here is a thoughtful look at the issue. Do you think Cofnas is on target?"
In case it is still not obvious (and this is the kind of thing which makes it hard for me to believe you are being sincere), I am referring to the suppression of views favoring a partial genetic contribution to group differences (see James Watson above, and controversy surrounding The Bell Curve book).Do you not see how weak that tweet is as an argument? Not to mention the complete lack of evidence presented.
How can you say "they have not been found and are unlikely to" given the progress we have seen in GWAS for these traits? Or is this some kind of all or nothing false dichotomy? And what do you even mean by "due to quantitative genetic models on human populations"? Due how? And which specific models?
P.S. In that last string of tweets, someone might want to explain to Ewan Birney about selective immigration and how that might affect ability gaps.
You think I am being insincere where in fact I am just applying the knowledge I have of the subject to the debate. Theodore for example, says gene flow would be irrelevant but every single paper and book I have read on phylogenetics and race argues the opposite. So when I stress it, it is not out of insincerity but rather because it is relevant and many here just hand wave it away.Right, but genotypically humans are very closely related. Ask a geneticist if you do not believe me. There are variations in phenotype, sometimes corresponding to "race" but that is not particularly informative of variations in genotype, rather it is mostly due to shared geographic ancestry. What I mean is that black people for example share a similar phenotype but are a paraphyletic group, with some African populations being closer to Eurasians than other African populations. If humans do not form a tree, then race is not informative of evolutionary relationships though. It is what systematics is all about. You will think I am being insincere again, but please open a systematics text or even a paper (for example about subspecies: https://academic.oup.com/sysbio/article-abstract/2/3/97/1674750?redirectedFrom=fulltext)
(I could not copy/paste from it the relevant excerpts unfortunately).But how do we find these genetic clusters? There are user dependent and there is no right answer to the number of K.
Is there any objective way of determining K? (Genuine question here, I really do not know. Recently however, Graham Coop released an updated version of his Popgen notes, and he states the same as I did)
Did you read the Lawson et al, 2018 paper?Ok, fair enough here. Though there is a way to test that. See this tweet for example which I had saved but forgot to link: https://twitter.com/itsbirdemic/status/1137021740373204992So if you are interested in continuing this discussion, what we can do is look at those intermediate populations and their allele frequencies. I think it is an objective way to test both Templeton's model of human evolution and the degree to which IBD explains the patterns of genetic variation in humans.Sure.
1. Human populations differ and there are biological correlates to our idea of race. If one defines race strictly by phenotype then the concept is most likely applicable to some extent.
2. There has been relatively little gene flow between Africa and Southeast Asia for example, and most likely none between the Americas and the Old world prior to the European colonization.
3. there are population differences in height, BMI and some medically-relevant traits. Generally, for traits of which we have evidence of directional selection and show high between population differentiation, differences correlate to some extent with ancestral populations or what you would call race.No, on the contrary, in topics where I do not know much (for example advanced genomics) going by expert consensus seems the reasonable thing to do.
(Responding as requested in your comment 108)
I think I have covered this adequately in other comments.
It is relevant, but the remaining observable differences (as Greg Cochran argues) make clear that gene flow has not been sufficient to eliminate the significant variation we see.
bolded – Are you kidding me? Which of those phenotypic variations are NOT due to genes? Skin color? Hair type and color?
italics – As far as I am concerned that and race are a distinction without a difference.
Examples? And don’t play games with North Africans who clearly group separately from sub-Saharan Africans.
The question is to what degree is a tree representation accurate. Please stop with the false dichotomies. Either you are an extremely sloppy thinker or think I am.
We have very different ideas of which references and arguments we find credible.
We can look visually at the clustering to get some idea. Beyond that, yes there are methods, but as you note they are imperfect. Which is not at all the same as useless or meaningless (more false dichotomies, don’t let the perfect be the enemy of the good).
There are objective methods, but cherry picking between them can allow subjectivity to creep in. See the “Determining Optimal Number of Clusters” at https://towardsdatascience.com/10-tips-for-choosing-the-optimal-number-of-clusters-277e93d72d92
Link papers if you want me to respond.
Did you happen to notice that Bird included no evidence for his position? Evidence matters.
1. Phenotype is related to genotype.
2. So do those splits with little gene flow work as demarcations for groups?
3. And skin color. And hair type. And pygmy height… Yet somehow this correlation is not enough to make “what you would call race” a usable construct. Interesting.
It is. Except when the experts quite consistently ignore provocative points (e.g. Graham Coop, you might try reading between the lines of what he says and doesn’t say a bit more, what I like about him is he seems to stick to the truth) or else actively lie and misrepresent (e.g. Ewan Birney and Kevin Bird) IMO.
Genetic clustering algorithms, implemented in programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans as a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups that do not have admixture in their recent history, where recent genetic drift is strong or that deviate in other ways from the underlying inference model. Unfortunately, such histories can be misleading. We have implemented an approach, badMIXTURE, to assess the goodness of fit of the model using the ancestry “palettes” estimated by CHROMOPAINTER and apply it to both simulated data and real case studies. Combining these complementary analyses with additional methods that are designed to test specific hypotheses allows a richer and more robust analysis of recent demographic history.I will look up studies on Middle Easterners or other intermediate populations and let you know. However, in all honesty, that paper has it wrong to an extent. They are supposed to be between Europeans and Africans not between Africans and East Asians. But my point was that by finding similar studies it is possible to test if Templeton is right or wrong for example.Not always. https://www.biorxiv.org/content/10.1101/773663v2
Source populations for an admixed population can possess distinct patterns of genotype and phenotype at the beginning of the admixture process. Such differences are sometimes taken to serve as markers of ancestry---that is, phenotypes that are initially associated with the ancestral background in one source population are taken to reflect ancestry in that population. Examples exist, however, in which genotypes or phenotypes initially associated with ancestry in one source population have decoupled from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. We develop a mechanistic model for describing the joint dynamics of admixture levels and phenotype distributions in an admixed population. The approach includes a quantitative-genetic model that relates a phenotype to underlying loci that affect its trait value. We consider three forms of mating. First, individuals might assort in a manner that is independent of the overall genetic admixture level. Second, individuals might assort by a quantitative phenotype that is initially correlated with the genetic admixture level. Third, individuals might assort by the genetic admixture level itself. Under the model, we explore the relationship between genetic admixture level and phenotype over time, studying the effect on this relationship of the genetic architecture of the phenotype. We find that the decoupling of genetic ancestry and phenotype can occur surprisingly quickly, especially if the phenotype is driven by a small number of loci. We also find that positive assortative mating attenuates the process of dissociation in relation to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype. The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might be a reliable proxy for ancestry for only a short time, especially if the trait is determined by relatively few loci. The results are potentially relevant in admixed human populations, in which phenotypes that have a perceived correlation with ancestry might have social significance as ancestry markers, despite declining correlations with ancestry over time.
Arbitrary but sure I can agree on that. Groups are not necessarily races though, unless you use race differently than I do.Race is a stronger term than phenotypic differences in those traits, is all I am saying.Are you sure we are talking about the same person?
https://www.pnas.org/content/111/35/E3596My position is that though they are biological correlates to race, race does not match the patterns of genetic diversity we see in worldwide human populations. Pretty much what these two tweets are saying: https://twitter.com/itsbirdemic/status/1222353680160215040
What would be your counter argument to that?res, my whole point is that there is no such thing as unmixed Africans, East Asians and Europeans.
Europeans for example are a mix of people closely related to modern-day Middle Easterners (which you guys think mixed rather than ancestral to Europeans) , local hunter-gatherers and Siberians from the north (Ancient North Eurasians).
Is your argument that these 3 populations were entirely West Eurasian or isolated from Africans or East Asians?
If indeed there are unmixed Europeans, Africans and East Asians (we can test that) or if ancient DNA shows different origins than I have presented above, then I am willing to admit races exist.Fine, forget the intermediate groups, lets focus on Europeans, Africans and East Asians as you say.Tell David Reich and Graham Coop that. Come on, you can not really believe they are just pretending or ignorant about the science.Fair enough, I am too I guess, but as you see willing to bypass any political motivations etc. I only brought it up because you did so before.Did he have evidence to back up his assertions? Did he put it in print? And actually, no, though I do not share his opinion I understand this is a politically charged topic and disagree with how he was treated. But don't forget, he has a history of making controversial statements and likes to provoke people. Ask geneticists who worked with him or know him. (So I have been told at least)Not you or Steve Sailer but @theodore and @mikemikev seemed to assert that. Asserting race=subspecies means it exists objectively and less so because of social construction (all taxonomy is constructed of course but that is a different story)Disagree that what is happening?Largely yes, though Reich did not assert what he claims he did. At least not any more after his newest papers.
Cofnas is saying these variants are likely to be found. Sure, but my point is they have not been found and are unlikely to, due to quantitative genetic models on human populations.(quick example for differential selection not being a good argument: https://twitter.com/ewanbirney/status/1221975246695063553
We can expand on that, but I do not want to gish-gallop this conversation. Also, I would appreciate if you could answer my comment #102.
Here is the full text of that tweet: “Exactly the question isn’t how some arbitrary divisions compare to socially constructed categories but how well do those socially constructed categories actually match patterns of genetic diversity. We know they don’t match them very well at all!”
I’ll consider giving a counterargument if you provide something that contains an actual argument and/or evidence rather than a simple assertion. Do you not understand how pathetic it is to introduce tweets like that into an attempt to have a serious evidence based discussion?
Fair enough. We are talking about two very different things.
1. How the different groups got to where they are today. Which is as you say a long chain of complex mixing.
2. Where the groups are today as shown by the clustering in the PCA plots.
When I talk about “unmixed” … I am referring to individuals who clearly group into their respective clusters. As opposed to those who are mixed race (children of individuals of two different races). There is a third case–intermediate populations that form their own relatively stable intermediate groups. You focus on that third case all of the time, but the point of my PCA plot comments is that there are relatively few people like that compared to the numbers in the major clusters.
Do you deny that there are many people who clearly group into African, East Asian, and European clusters on PCA plots? Albeit obscured somewhat by overplotting in most plots we see.
Thanks. That will help this conversation be more concrete and meaningful.
Not them. They are two of the more truthful people I see out there. But both are very careful about what they do and do not say. And even given that, David Reich is walking a fine line.
And speaking of fine lines, it will be interesting to see if Kevin Bird gets cancelled over his recent paper showing African-European EDU PGS differences are partially genetic. You like citing him as a reference. Do you agree with him about that?
https://www.unz.com/isteve/the-mismeasure-of-genes/
When I say pretense I am often including the willful ignoring of controversial areas (with a subcategory of neither agreeing with nor criticizing people who repeat the party line, see Graham Coop’s exchanges with people like Ewan Birney on Twitter). Which perhaps isn’t strictly accurate, but IMHO close enough for most purposes.
But you do agree that Watson is an object lesson in what can happen even to the most respected of scientists if he says something wrong about group differences, right? Given that, how can I (or you!) take anything a scientist says in public on these topics without a great deal of skepticism?
When you find yourself asking questions like this please consider rereading the immediately preceding and following sentences. Here is more complete context: “The problem I am describing is real. Do you sincerely disagree this is happening? Here is a thoughtful look at the issue. Do you think Cofnas is on target?”
In case it is still not obvious (and this is the kind of thing which makes it hard for me to believe you are being sincere), I am referring to the suppression of views favoring a partial genetic contribution to group differences (see James Watson above, and controversy surrounding The Bell Curve book).
Do you not see how weak that tweet is as an argument? Not to mention the complete lack of evidence presented.
How can you say “they have not been found and are unlikely to” given the progress we have seen in GWAS for these traits? Or is this some kind of all or nothing false dichotomy? And what do you even mean by “due to quantitative genetic models on human populations”? Due how? And which specific models?
P.S. In that last string of tweets, someone might want to explain to Ewan Birney about selective immigration and how that might affect ability gaps.
I can cite you papers like this: https://muse.jhu.edu/article/381884/pdf?casa_token=_09_Yn-UFgQAAAAA:rXcKpbFjoPp-HG6lguB25FMcIc62CfqkvuGqAXtQuIQsGXAxFtgFNN_CeXim-2kqfevpI71eEA but it is likely you will handwave it away as being irrelevant, am I wrong?
In any case, here is a more clear example: Are blacks a race?Indeed, it would seem many of our disagreements stem from interpreting terms differently or talking about different things.Right, but I am open to evidence that this mixing was not as extensive as I think it was (rather read it was). But my comment was more so about Middle Easterners for example, traditionally considered mixed race between Europeans and Africans when in reality Europeans are mixed race between Middle Easterners and people native to Europe and Siberia.
So why pick out Europeans as a race instead of middle Easterners?
https://www.nature.com/articles/nature14317sure, but (and it is an honest question) why pick Europeans, East Asians and Africans (by that I am assuming Bantu speakers- the dominant ancestral component from West Africa to South Africa)? Why not pick Middle Easterners as the ancestral population for example like I said above?No, I do not deny that. My two points of disagreement are 1. why pick those populations? 2. is it enough to call them races when the term usually means subspecies?They are but they do not support HBD in any way. Only David Reich hinted that races might exist but Graham Coop has published many papers against HBD and a big chunk of them and papers from other people in his lab are included in the newest paper against the hereditarian hypothesis by Kevin Bird.That is not exactly what he said but sure, its possible some of the IQ gap to be genetic. I am not a psychometrician and I do not know how robust is the science of IQ in the first place, though evidence suggests it is.Right, but they also publish papers with evidence against a major genetic component in group differences and races in humans. And like I said, we can disregard what they say, but where does the written peer-reviewed evidence points to?
You often cited Piffer's paper for example but there are many reasons (I can cite relevant papers here) to be skeptical of his results.My question was not out of insincerity but rather misunderstanding the sentence above that. Its clear now, thanks.Well, no, why is it weak? I cited a paper above about the mixing that led to Europeans, is there any evidence that would not need a complex selection pressure to justify higher genetic IQ?
Unless, all these 3 populations were closely related to begin with, I am not sure.All right, I will expand on what I mean:
Basically this paper is what I mean by quantitative genetic models:https://digitalcommons.wayne.edu/cgi/viewcontent.cgi?referer=https://scholar.google.com/&httpsredir=1&article=1107&context=humbiol_preprints
(long paper and I myself dont understand the math well, however just take a look at the abstract if you want -their main model is in this study: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516610/
Researchers in many fields have considered the meaning of two results about genetic variation for concepts of “race.” First, at most genetic loci, apportionments of human genetic diversity find that worldwide populations are genetically similar. Second, when multiple genetic loci are examined, it is possible to distinguish people with ancestry from different geographical regions. These two results raise an important question about human phenotypic diversity: To what extent do populations typically differ on phenotypes determined by multiple genetic loci? It might be expected that such phenotypes follow the pattern of similarity observed at individual loci. Alternatively, because they have a multilocus genetic architecture, they might follow the pattern of greater differentiation suggested by multilocus ancestry inference. To address the question, we extend a well-known classification model of Edwards (2003) by adding a selectively neutral quantitative trait. Using the extended model, we show, in line with previous work in quantitative genetics, that regardless of how many genetic loci influence the trait, one neutral trait is approximately as informative about ancestry as a single genetic locus. The results support the relevance of single-locus genetic-diversity partitioning for predictions about phenotypic diversity.
In addition, regarding the use of PGS: https://www.genetics.org/content/208/4/1351
In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to several human examples (Racimo et al. 2018). By definition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary geneticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide association studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for changes in allele frequencies. By aggregating small signals of change across many such loci, directional natural selection is now in principle detectable using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accompanying test of polygenic selection. However, it is important to be aware of complications that arise in interpretation, especially given that these studies may easily be misinterpreted both in and outside the evolutionary genetics community. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are interpreted and reported upon more broadly.
PS: Regarding my mention of Middle Easterners, I do not want to derail from talking about the 3 populations we agreed upon earlier. However, it is a question I sincerely had for a while and perhaps you can give me a good argument as to why pick Europeans instead.
I'll consider giving a counterargument if you provide something that contains an actual argument and/or evidence rather than a simple assertion. Do you not understand how pathetic it is to introduce tweets like that into an attempt to have a serious evidence based discussion?Fair enough. We are talking about two very different things.
1. How the different groups got to where they are today. Which is as you say a long chain of complex mixing.
2. Where the groups are today as shown by the clustering in the PCA plots.
When I talk about "unmixed" ... I am referring to individuals who clearly group into their respective clusters. As opposed to those who are mixed race (children of individuals of two different races). There is a third case--intermediate populations that form their own relatively stable intermediate groups. You focus on that third case all of the time, but the point of my PCA plot comments is that there are relatively few people like that compared to the numbers in the major clusters.
Do you deny that there are many people who clearly group into African, East Asian, and European clusters on PCA plots? Albeit obscured somewhat by overplotting in most plots we see.Thanks. That will help this conversation be more concrete and meaningful.Not them. They are two of the more truthful people I see out there. But both are very careful about what they do and do not say. And even given that, David Reich is walking a fine line.
And speaking of fine lines, it will be interesting to see if Kevin Bird gets cancelled over his recent paper showing African-European EDU PGS differences are partially genetic. You like citing him as a reference. Do you agree with him about that?
https://www.unz.com/isteve/the-mismeasure-of-genes/
When I say pretense I am often including the willful ignoring of controversial areas (with a subcategory of neither agreeing with nor criticizing people who repeat the party line, see Graham Coop's exchanges with people like Ewan Birney on Twitter). Which perhaps isn't strictly accurate, but IMHO close enough for most purposes.But you do agree that Watson is an object lesson in what can happen even to the most respected of scientists if he says something wrong about group differences, right? Given that, how can I (or you!) take anything a scientist says in public on these topics without a great deal of skepticism?When you find yourself asking questions like this please consider rereading the immediately preceding and following sentences. Here is more complete context: "The problem I am describing is real. Do you sincerely disagree this is happening? Here is a thoughtful look at the issue. Do you think Cofnas is on target?"
In case it is still not obvious (and this is the kind of thing which makes it hard for me to believe you are being sincere), I am referring to the suppression of views favoring a partial genetic contribution to group differences (see James Watson above, and controversy surrounding The Bell Curve book).Do you not see how weak that tweet is as an argument? Not to mention the complete lack of evidence presented.
How can you say "they have not been found and are unlikely to" given the progress we have seen in GWAS for these traits? Or is this some kind of all or nothing false dichotomy? And what do you even mean by "due to quantitative genetic models on human populations"? Due how? And which specific models?
P.S. In that last string of tweets, someone might want to explain to Ewan Birney about selective immigration and how that might affect ability gaps.
Have I not done so already previously?
I can cite you papers like this: https://muse.jhu.edu/article/381884/pdf?casa_token=_09_Yn-UFgQAAAAA:rXcKpbFjoPp-HG6lguB25FMcIc62CfqkvuGqAXtQuIQsGXAxFtgFNN_CeXim-2kqfevpI71eEA but it is likely you will handwave it away as being irrelevant, am I wrong?
In any case, here is a more clear example: Are blacks a race?
Indeed, it would seem many of our disagreements stem from interpreting terms differently or talking about different things.
Right, but I am open to evidence that this mixing was not as extensive as I think it was (rather read it was). But my comment was more so about Middle Easterners for example, traditionally considered mixed race between Europeans and Africans when in reality Europeans are mixed race between Middle Easterners and people native to Europe and Siberia.
So why pick out Europeans as a race instead of middle Easterners?
https://www.nature.com/articles/nature14317
sure, but (and it is an honest question) why pick Europeans, East Asians and Africans (by that I am assuming Bantu speakers- the dominant ancestral component from West Africa to South Africa)? Why not pick Middle Easterners as the ancestral population for example like I said above?
No, I do not deny that. My two points of disagreement are 1. why pick those populations? 2. is it enough to call them races when the term usually means subspecies?
They are but they do not support HBD in any way. Only David Reich hinted that races might exist but Graham Coop has published many papers against HBD and a big chunk of them and papers from other people in his lab are included in the newest paper against the hereditarian hypothesis by Kevin Bird.
That is not exactly what he said but sure, its possible some of the IQ gap to be genetic. I am not a psychometrician and I do not know how robust is the science of IQ in the first place, though evidence suggests it is.
Right, but they also publish papers with evidence against a major genetic component in group differences and races in humans. And like I said, we can disregard what they say, but where does the written peer-reviewed evidence points to?
You often cited Piffer’s paper for example but there are many reasons (I can cite relevant papers here) to be skeptical of his results.
My question was not out of insincerity but rather misunderstanding the sentence above that. Its clear now, thanks.
Well, no, why is it weak? I cited a paper above about the mixing that led to Europeans, is there any evidence that would not need a complex selection pressure to justify higher genetic IQ?
Unless, all these 3 populations were closely related to begin with, I am not sure.
All right, I will expand on what I mean:
Basically this paper is what I mean by quantitative genetic models:https://digitalcommons.wayne.edu/cgi/viewcontent.cgi?referer=https://scholar.google.com/&httpsredir=1&article=1107&context=humbiol_preprints
(long paper and I myself dont understand the math well, however just take a look at the abstract if you want -their main model is in this study: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516610/
Researchers in many fields have considered the meaning of two results about genetic variation for concepts of “race.” First, at most genetic loci, apportionments of human genetic diversity find that worldwide populations are genetically similar. Second, when multiple genetic loci are examined, it is possible to distinguish people with ancestry from different geographical regions. These two results raise an important question about human phenotypic diversity: To what extent do populations typically differ on phenotypes determined by multiple genetic loci? It might be expected that such phenotypes follow the pattern of similarity observed at individual loci. Alternatively, because they have a multilocus genetic architecture, they might follow the pattern of greater differentiation suggested by multilocus ancestry inference. To address the question, we extend a well-known classification model of Edwards (2003) by adding a selectively neutral quantitative trait. Using the extended model, we show, in line with previous work in quantitative genetics, that regardless of how many genetic loci influence the trait, one neutral trait is approximately as informative about ancestry as a single genetic locus. The results support the relevance of single-locus genetic-diversity partitioning for predictions about phenotypic diversity.
In addition, regarding the use of PGS: https://www.genetics.org/content/208/4/1351
In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to several human examples (Racimo et al. 2018). By definition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary geneticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide association studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for changes in allele frequencies. By aggregating small signals of change across many such loci, directional natural selection is now in principle detectable using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accompanying test of polygenic selection. However, it is important to be aware of complications that arise in interpretation, especially given that these studies may easily be misinterpreted both in and outside the evolutionary genetics community. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are interpreted and reported upon more broadly.
PS: Regarding my mention of Middle Easterners, I do not want to derail from talking about the 3 populations we agreed upon earlier. However, it is a question I sincerely had for a while and perhaps you can give me a good argument as to why pick Europeans instead.
I choose Africans, East Asians, and Europeans as my base groups because that is quite clearly indicated by the PCA plots (this is obvious to you, right?). Why that is so is an interesting question (and I think has interesting implications for your contention about Middle Easterners), but is not what I want to talk about here.1. Covered above.
2. I call them races because that is the historical usage. As far as the subspecies equivalence, that seems like a fairly recent notion courtesy of obfuscators like you. I don't really care what we call them. If you are so traumatized by my usage of race (which I believe is in line with how it has been used for centuries) then how about we just call them "ancestral populations"? I really don't care and consider your going on about this a giant waste of time.Of course they don't support HBD. Do you think they want to be Watsoned?Examples? I would not be quick to hang your hat on Kevin Bird's paper, BTW.There is a great deal of skepticism out there. The general technique used by the critics is one I like to call FUD (and there is some truth there, e.g. LD and cross-population use of PGS scores). But I still have yet to see a convincing explanation of why he sees such high correlations. 0.9 correlations are an awfully big coincidence. Especially when they happen over and over with different sets of SNPs. Aren't you the least little bit curious about why he keeps seeing the same result?Here is the tweet I called weak: https://twitter.com/ewanbirney/status/1221975246695063553
and the text of it: "Great work Kevin. @aylwyn_scally and myself found similar things to you - IQ genetics looks reasonable “humdrum” as quantitative trait. In addition natural selection for IQ in “Europeans” would have a complex selection pattern given the admixture of Anatolian/Yamnaya/H. gathers"
I see no evidence or argument. Hence weak. I'm not even sure I understand what your second sentence means, but I am pretty sure it is not worthwhile for this conversation. Complex seems like a meaningless adjective to apply to selection pressure. And what does it mean to call IQ genetics "humdrum"?
Do you have any idea how tedious this conversation is for me? Rather than going on and on like this how about spending that time responding to the PCA points as you keep promising to do?I don't see how that counters in any way the findings of various SNPs in IQ GWAS.Same. In particular, notice that they assume "a selectively neutral quantitative trait." That hardly holds for IQ. Or are we back to you claiming IQ has not been selected for in humans?Same. That in no way negates the SNPs having been found. It does rightly emphasize that there should be some caution in interpretation. Some of the SNPs will probably turn out to be spurious. But it is unlikely all of them will. Especially given the tendency we see of them to be related to the brain.
Rather than throwing three barely relevant papers at me, how about trying for just one straight answer?See the PCA plot statement earlier in this comment.
italics - As far as I am concerned that and race are a distinction without a difference.Examples? And don't play games with North Africans who clearly group separately from sub-Saharan Africans.The question is to what degree is a tree representation accurate. Please stop with the false dichotomies. Either you are an extremely sloppy thinker or think I am.
We have very different ideas of which references and arguments we find credible.We can look visually at the clustering to get some idea. Beyond that, yes there are methods, but as you note they are imperfect. Which is not at all the same as useless or meaningless (more false dichotomies, don't let the perfect be the enemy of the good).There are objective methods, but cherry picking between them can allow subjectivity to creep in. See the "Determining Optimal Number of Clusters" at https://towardsdatascience.com/10-tips-for-choosing-the-optimal-number-of-clusters-277e93d72d92Link papers if you want me to respond.Did you happen to notice that Bird included no evidence for his position? Evidence matters.1. Phenotype is related to genotype.
2. So do those splits with little gene flow work as demarcations for groups?
3. And skin color. And hair type. And pygmy height... Yet somehow this correlation is not enough to make "what you would call race" a usable construct. Interesting.It is. Except when the experts quite consistently ignore provocative points (e.g. Graham Coop, you might try reading between the lines of what he says and doesn't say a bit more, what I like about him is he seems to stick to the truth) or else actively lie and misrepresent (e.g. Ewan Birney and Kevin Bird) IMO.
Fair enough, but had not read them yet when I replied.
Greg Cochran argues without having read enough of the literature it seems. Not all traits show the same directional selection that skin color for example does.
They are due to genes but they are not informative of overall genomic differentiation.
Well, no. You need common genetic ancestry not only geographic ancestry. Selection can act on polyphyletic populations. (think of the phenotype of Melanesians and Africans even though genomically they are as distant as you can get)
Is there a paper discussing an optimal number for human populations? If there is one that did that (unless you already cited one and I missed it, then fair enough)
https://www.nature.com/articles/s41467-018-05257-7
Genetic clustering algorithms, implemented in programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans as a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups that do not have admixture in their recent history, where recent genetic drift is strong or that deviate in other ways from the underlying inference model. Unfortunately, such histories can be misleading. We have implemented an approach, badMIXTURE, to assess the goodness of fit of the model using the ancestry “palettes” estimated by CHROMOPAINTER and apply it to both simulated data and real case studies. Combining these complementary analyses with additional methods that are designed to test specific hypotheses allows a richer and more robust analysis of recent demographic history.
I will look up studies on Middle Easterners or other intermediate populations and let you know. However, in all honesty, that paper has it wrong to an extent. They are supposed to be between Europeans and Africans not between Africans and East Asians. But my point was that by finding similar studies it is possible to test if Templeton is right or wrong for example.
Not always. https://www.biorxiv.org/content/10.1101/773663v2
Source populations for an admixed population can possess distinct patterns of genotype and phenotype at the beginning of the admixture process. Such differences are sometimes taken to serve as markers of ancestry—that is, phenotypes that are initially associated with the ancestral background in one source population are taken to reflect ancestry in that population. Examples exist, however, in which genotypes or phenotypes initially associated with ancestry in one source population have decoupled from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. We develop a mechanistic model for describing the joint dynamics of admixture levels and phenotype distributions in an admixed population. The approach includes a quantitative-genetic model that relates a phenotype to underlying loci that affect its trait value. We consider three forms of mating. First, individuals might assort in a manner that is independent of the overall genetic admixture level. Second, individuals might assort by a quantitative phenotype that is initially correlated with the genetic admixture level. Third, individuals might assort by the genetic admixture level itself. Under the model, we explore the relationship between genetic admixture level and phenotype over time, studying the effect on this relationship of the genetic architecture of the phenotype. We find that the decoupling of genetic ancestry and phenotype can occur surprisingly quickly, especially if the phenotype is driven by a small number of loci. We also find that positive assortative mating attenuates the process of dissociation in relation to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype. The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might be a reliable proxy for ancestry for only a short time, especially if the trait is determined by relatively few loci. The results are potentially relevant in admixed human populations, in which phenotypes that have a perceived correlation with ancestry might have social significance as ancestry markers, despite declining correlations with ancestry over time.
Arbitrary but sure I can agree on that. Groups are not necessarily races though, unless you use race differently than I do.
Race is a stronger term than phenotypic differences in those traits, is all I am saying.
Are you sure we are talking about the same person?
How about refuting it there? If he won't post your response then post it here and we can discuss whether he is being reasonable or not.What does that even mean? They are examples of overall genomic differentiation. How is that not informative?
(If this is typical of your field I am really glad I don't have to read anthropology papers)I thought you were just arguing that those two were synonymous? What really matters for race is the genetic ancestry, but the geographic ancestry serves as a decent proxy.
And how is your last sentence even relevant to this issue?Don't let the perfect be the enemy of the good. I thought you had agreed to work with Africans, East Asians, and Europeans as groups? Let's do that--which would be k=3.I don't see how that is relevant. If you are going to endlessly spam papers and abstracts of doubtful relevance then make clear the point you have in mind.I am going to file that away in the list of epic quotes from Anti-HBD. Yes, always. Genotype may not be completely determinative of phenotype, but it is always related. Or perhaps you would like it better if I said 99.9% percent of the time or some such? If so, give one concrete example where it is not related.
Please elaborate on how you think that paper supports your point. I am pretty sure it does not say what you think it says.How so? Your vagueness is tedious. Though it does make a good tell for when you think you are getting into deep water.
Perhaps you failed to notice the "..." in my statement? I was not limiting myself to just those traits.
You might want to spend some time learning about this fallacy: https://en.wikipedia.org/wiki/No_true_ScotsmanYes. As I asked in an earlier comment, how about showing me what he has to say about genetics and group differences in IQ (or height)? Surely he would be vigorously denouncing those ideas if they were untrue? And in peer reviewed research papers, not tweets.
P.S. Please respond to my PCA points. It is clear overplotting matters (and it has been 9 days since I made that point in comment 97). Admit it. And admit what that does to your clines vs. clusters argument in the PCA plot you provided. Your failure to do this is conclusive evidence of your insincerity as far as I am concerned. Stop wasting my time.
https://www.pnas.org/content/111/35/E3596My position is that though they are biological correlates to race, race does not match the patterns of genetic diversity we see in worldwide human populations. Pretty much what these two tweets are saying: https://twitter.com/itsbirdemic/status/1222353680160215040
What would be your counter argument to that?res, my whole point is that there is no such thing as unmixed Africans, East Asians and Europeans.
Europeans for example are a mix of people closely related to modern-day Middle Easterners (which you guys think mixed rather than ancestral to Europeans) , local hunter-gatherers and Siberians from the north (Ancient North Eurasians).
Is your argument that these 3 populations were entirely West Eurasian or isolated from Africans or East Asians?
If indeed there are unmixed Europeans, Africans and East Asians (we can test that) or if ancient DNA shows different origins than I have presented above, then I am willing to admit races exist.Fine, forget the intermediate groups, lets focus on Europeans, Africans and East Asians as you say.Tell David Reich and Graham Coop that. Come on, you can not really believe they are just pretending or ignorant about the science.Fair enough, I am too I guess, but as you see willing to bypass any political motivations etc. I only brought it up because you did so before.Did he have evidence to back up his assertions? Did he put it in print? And actually, no, though I do not share his opinion I understand this is a politically charged topic and disagree with how he was treated. But don't forget, he has a history of making controversial statements and likes to provoke people. Ask geneticists who worked with him or know him. (So I have been told at least)Not you or Steve Sailer but @theodore and @mikemikev seemed to assert that. Asserting race=subspecies means it exists objectively and less so because of social construction (all taxonomy is constructed of course but that is a different story)Disagree that what is happening?Largely yes, though Reich did not assert what he claims he did. At least not any more after his newest papers.
Cofnas is saying these variants are likely to be found. Sure, but my point is they have not been found and are unlikely to, due to quantitative genetic models on human populations.(quick example for differential selection not being a good argument: https://twitter.com/ewanbirney/status/1221975246695063553
We can expand on that, but I do not want to gish-gallop this conversation. Also, I would appreciate if you could answer my comment #102.
Wow are you still repeating these exact same points? It’s been months now.
You complain it has been months now, yet here you are.
Unless you actually care to contribute to the conversation with papers and arguments.
Genetic clustering algorithms, implemented in programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans as a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups that do not have admixture in their recent history, where recent genetic drift is strong or that deviate in other ways from the underlying inference model. Unfortunately, such histories can be misleading. We have implemented an approach, badMIXTURE, to assess the goodness of fit of the model using the ancestry “palettes” estimated by CHROMOPAINTER and apply it to both simulated data and real case studies. Combining these complementary analyses with additional methods that are designed to test specific hypotheses allows a richer and more robust analysis of recent demographic history.I will look up studies on Middle Easterners or other intermediate populations and let you know. However, in all honesty, that paper has it wrong to an extent. They are supposed to be between Europeans and Africans not between Africans and East Asians. But my point was that by finding similar studies it is possible to test if Templeton is right or wrong for example.Not always. https://www.biorxiv.org/content/10.1101/773663v2
Source populations for an admixed population can possess distinct patterns of genotype and phenotype at the beginning of the admixture process. Such differences are sometimes taken to serve as markers of ancestry---that is, phenotypes that are initially associated with the ancestral background in one source population are taken to reflect ancestry in that population. Examples exist, however, in which genotypes or phenotypes initially associated with ancestry in one source population have decoupled from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. We develop a mechanistic model for describing the joint dynamics of admixture levels and phenotype distributions in an admixed population. The approach includes a quantitative-genetic model that relates a phenotype to underlying loci that affect its trait value. We consider three forms of mating. First, individuals might assort in a manner that is independent of the overall genetic admixture level. Second, individuals might assort by a quantitative phenotype that is initially correlated with the genetic admixture level. Third, individuals might assort by the genetic admixture level itself. Under the model, we explore the relationship between genetic admixture level and phenotype over time, studying the effect on this relationship of the genetic architecture of the phenotype. We find that the decoupling of genetic ancestry and phenotype can occur surprisingly quickly, especially if the phenotype is driven by a small number of loci. We also find that positive assortative mating attenuates the process of dissociation in relation to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype. The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might be a reliable proxy for ancestry for only a short time, especially if the trait is determined by relatively few loci. The results are potentially relevant in admixed human populations, in which phenotypes that have a perceived correlation with ancestry might have social significance as ancestry markers, despite declining correlations with ancestry over time.
Arbitrary but sure I can agree on that. Groups are not necessarily races though, unless you use race differently than I do.Race is a stronger term than phenotypic differences in those traits, is all I am saying.Are you sure we are talking about the same person?
Re Graham Coop: He is one of the first geneticists to speak against HBD claims usually, hence why I find weird that you bring him up as trying to say something else between the lines.
P.S. That tweet you linked makes a good point, but I think he leaves it overly broad in a way which serves his agenda. A key distinction for whether discrimination can be involved is which specific outcome variables are involved. So if you are looking at the linkage between a height PGS and employment then discrimination can be relevant. But if you are looking at the relationship between a height PGS and phenotypic height (which seems to be his implication) then discrimination impact is much harder to credit (perhaps as a second order environmental effect due to discrimination against short parents depriving them of resources, but that is a reach). I actually don't think he rebutted the primary point at all about PGS helping with making the distinction between innate and environmental causes.
Please, more of those though and less Kevin Bird, Adam Rutherford, and Ewan Birney blather.
I don’t see the contradiction. You’ve been repeating the same facile assertions for months, ignoring the data and definition based responses, and repeating the same assertions. And here I am saying that. Do you mean that me spending a few minutes here is a small victory for your time wasting exercise?
Why have you still not replied to my last posts to you?
Definition-based responses mean that you are just re-defining the term.
I am not ignoring data-based responses when I see such responses to have merit. You would see that if you read more carefully.
I have myself posted many papers and data points, have you considered them? Have you changed your mind on anything you previously believed about race?
What victory? What are you talking about?
This is the kind of lunatic gibberish you write and expect people to take you seriously. Are we supposed to discuss concepts without definitions? All you do is type gibberish and post random URLs, then declare yourself the winner when people stop bothering to respond to you.
He clearly is fighting the good fight (as you and he see it). Can you find any explicit commentary from him about group genetic differences and IQ? Dogs that don’t bark can be valuable clues (just ask Sherlock Holmes).
P.S. That tweet you linked makes a good point, but I think he leaves it overly broad in a way which serves his agenda. A key distinction for whether discrimination can be involved is which specific outcome variables are involved. So if you are looking at the linkage between a height PGS and employment then discrimination can be relevant. But if you are looking at the relationship between a height PGS and phenotypic height (which seems to be his implication) then discrimination impact is much harder to credit (perhaps as a second order environmental effect due to discrimination against short parents depriving them of resources, but that is a reach). I actually don’t think he rebutted the primary point at all about PGS helping with making the distinction between innate and environmental causes.
Please, more of those though and less Kevin Bird, Adam Rutherford, and Ewan Birney blather.
I can cite you papers like this: https://muse.jhu.edu/article/381884/pdf?casa_token=_09_Yn-UFgQAAAAA:rXcKpbFjoPp-HG6lguB25FMcIc62CfqkvuGqAXtQuIQsGXAxFtgFNN_CeXim-2kqfevpI71eEA but it is likely you will handwave it away as being irrelevant, am I wrong?
In any case, here is a more clear example: Are blacks a race?Indeed, it would seem many of our disagreements stem from interpreting terms differently or talking about different things.Right, but I am open to evidence that this mixing was not as extensive as I think it was (rather read it was). But my comment was more so about Middle Easterners for example, traditionally considered mixed race between Europeans and Africans when in reality Europeans are mixed race between Middle Easterners and people native to Europe and Siberia.
So why pick out Europeans as a race instead of middle Easterners?
https://www.nature.com/articles/nature14317sure, but (and it is an honest question) why pick Europeans, East Asians and Africans (by that I am assuming Bantu speakers- the dominant ancestral component from West Africa to South Africa)? Why not pick Middle Easterners as the ancestral population for example like I said above?No, I do not deny that. My two points of disagreement are 1. why pick those populations? 2. is it enough to call them races when the term usually means subspecies?They are but they do not support HBD in any way. Only David Reich hinted that races might exist but Graham Coop has published many papers against HBD and a big chunk of them and papers from other people in his lab are included in the newest paper against the hereditarian hypothesis by Kevin Bird.That is not exactly what he said but sure, its possible some of the IQ gap to be genetic. I am not a psychometrician and I do not know how robust is the science of IQ in the first place, though evidence suggests it is.Right, but they also publish papers with evidence against a major genetic component in group differences and races in humans. And like I said, we can disregard what they say, but where does the written peer-reviewed evidence points to?
You often cited Piffer's paper for example but there are many reasons (I can cite relevant papers here) to be skeptical of his results.My question was not out of insincerity but rather misunderstanding the sentence above that. Its clear now, thanks.Well, no, why is it weak? I cited a paper above about the mixing that led to Europeans, is there any evidence that would not need a complex selection pressure to justify higher genetic IQ?
Unless, all these 3 populations were closely related to begin with, I am not sure.All right, I will expand on what I mean:
Basically this paper is what I mean by quantitative genetic models:https://digitalcommons.wayne.edu/cgi/viewcontent.cgi?referer=https://scholar.google.com/&httpsredir=1&article=1107&context=humbiol_preprints
(long paper and I myself dont understand the math well, however just take a look at the abstract if you want -their main model is in this study: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516610/
Researchers in many fields have considered the meaning of two results about genetic variation for concepts of “race.” First, at most genetic loci, apportionments of human genetic diversity find that worldwide populations are genetically similar. Second, when multiple genetic loci are examined, it is possible to distinguish people with ancestry from different geographical regions. These two results raise an important question about human phenotypic diversity: To what extent do populations typically differ on phenotypes determined by multiple genetic loci? It might be expected that such phenotypes follow the pattern of similarity observed at individual loci. Alternatively, because they have a multilocus genetic architecture, they might follow the pattern of greater differentiation suggested by multilocus ancestry inference. To address the question, we extend a well-known classification model of Edwards (2003) by adding a selectively neutral quantitative trait. Using the extended model, we show, in line with previous work in quantitative genetics, that regardless of how many genetic loci influence the trait, one neutral trait is approximately as informative about ancestry as a single genetic locus. The results support the relevance of single-locus genetic-diversity partitioning for predictions about phenotypic diversity.
In addition, regarding the use of PGS: https://www.genetics.org/content/208/4/1351
In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to several human examples (Racimo et al. 2018). By definition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary geneticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide association studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for changes in allele frequencies. By aggregating small signals of change across many such loci, directional natural selection is now in principle detectable using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accompanying test of polygenic selection. However, it is important to be aware of complications that arise in interpretation, especially given that these studies may easily be misinterpreted both in and outside the evolutionary genetics community. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are interpreted and reported upon more broadly.
PS: Regarding my mention of Middle Easterners, I do not want to derail from talking about the 3 populations we agreed upon earlier. However, it is a question I sincerely had for a while and perhaps you can give me a good argument as to why pick Europeans instead.
You have posted a combination of papers and tweets. When you post a tweet which contains an assertion without an argument or evidence and ask me for a response it is perfectly reasonable for me to make the response I did. And what you have posted elsewhere about whatever else does not really matter towards that particular point. Having to respond to stupid evasions like that from you is a big part of what makes you seem insincere.
Not sure how many times I need to say this before you take it to heart, but if you want me to engage with your links give me an excerpt and/or (preferably and) comment which give an idea of the point you are trying to make and how your source supports it. I think I do this for you. Please return the favor.
Yes. And in that particular example you took what I was referring to and took it in a completely different direction. Please stop doing that. It is annoying. If you don’t understand what definition I have in mind please ask rather than just asserting something completely different.
This should be obvious, so hopefully I won’t need to say it more than once. Even though you repeat that particular question multiple times in your comment.
I choose Africans, East Asians, and Europeans as my base groups because that is quite clearly indicated by the PCA plots (this is obvious to you, right?). Why that is so is an interesting question (and I think has interesting implications for your contention about Middle Easterners), but is not what I want to talk about here.
1. Covered above.
2. I call them races because that is the historical usage. As far as the subspecies equivalence, that seems like a fairly recent notion courtesy of obfuscators like you. I don’t really care what we call them. If you are so traumatized by my usage of race (which I believe is in line with how it has been used for centuries) then how about we just call them “ancestral populations”? I really don’t care and consider your going on about this a giant waste of time.
Of course they don’t support HBD. Do you think they want to be Watsoned?
Examples? I would not be quick to hang your hat on Kevin Bird’s paper, BTW.
There is a great deal of skepticism out there. The general technique used by the critics is one I like to call FUD (and there is some truth there, e.g. LD and cross-population use of PGS scores). But I still have yet to see a convincing explanation of why he sees such high correlations. 0.9 correlations are an awfully big coincidence. Especially when they happen over and over with different sets of SNPs. Aren’t you the least little bit curious about why he keeps seeing the same result?
Here is the tweet I called weak: https://twitter.com/ewanbirney/status/1221975246695063553
and the text of it: “Great work Kevin. @aylwyn_scally and myself found similar things to you – IQ genetics looks reasonable “humdrum” as quantitative trait. In addition natural selection for IQ in “Europeans” would have a complex selection pattern given the admixture of Anatolian/Yamnaya/H. gathers”
I see no evidence or argument. Hence weak. I’m not even sure I understand what your second sentence means, but I am pretty sure it is not worthwhile for this conversation. Complex seems like a meaningless adjective to apply to selection pressure. And what does it mean to call IQ genetics “humdrum”?
Do you have any idea how tedious this conversation is for me? Rather than going on and on like this how about spending that time responding to the PCA points as you keep promising to do?
I don’t see how that counters in any way the findings of various SNPs in IQ GWAS.
Same. In particular, notice that they assume “a selectively neutral quantitative trait.” That hardly holds for IQ. Or are we back to you claiming IQ has not been selected for in humans?
Same. That in no way negates the SNPs having been found. It does rightly emphasize that there should be some caution in interpretation. Some of the SNPs will probably turn out to be spurious. But it is unlikely all of them will. Especially given the tendency we see of them to be related to the brain.
Rather than throwing three barely relevant papers at me, how about trying for just one straight answer?
See the PCA plot statement earlier in this comment.
These data made it possible to see how FST played out when no one could dispute taxonomic and genetic significance. The answer surprised us. FST was pretty close to the canonical 0.15 shown so many times for human populations. In our analysis, FST was 0.12 for humans, but for humans and chimpanzees together, FST rose only to 0.18. Indeed, we found one locus, D13S122, where the size range of human and chimpanzee alleles hardly overlapped, yet FST equaled 0.15 (Figure 1). We ultimately found that the genetic and statistical model underlying FST does not fit well to human populations. Specifically, human population structure strongly biases the outcome of analyses by violating two assumptions: first, that expected genetic diversity is the same in every population; and second, that divergence between all pairs of populations is equal and independent
I am citing that in response to arguments based on Fst that Greg Cochran and other HBD people often like to make. It is not a very useful measure for human taxonomy.I do not do it on purpose any more than you do. It probably stems that the papers I read use them differently often times than you use them here.It is an interesting question. It would also seem as Middle Easterners are mixed with populations Europeans are not if we go strictly by PCA. However caution is needed when interpreting PCAs.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989108/
They interpreted these patterns as resulting from specific migration events, such as the migration of agriculturalists out of the Near East [1, 2, 3]. Cavalli-Sforza et al’s results have been highly influential (e.g. [4]), and controversial [5, 6, 7, 8, 9], and PCA has become heavily used in population genetics (e.g. [10, 11, 12, 13]). Despite its widespread use, the behavior of PCA with data exhibiting continuous spatial variation, such as might exist within human continental groups, has been little studied. Here, using empirical and theoretical approaches, we find that the distinctive patterns observed by Cavalli-Sforza et al resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns are not necessarily due to population movements.
On that point I think LL-CS was correct, but what I am trying to say is that position on a PCA might reflect other scenarios rather than gene flow or demographic history.If you do not think of them are subspecies, it is easier to agree with you on what race is. Ancestral populations is not a term I have a lot of issues with.I brought this up because you implied they do behind the lines somewhere and I have not seen evidence that is the case (with the possible exception of David Reich)Poor choice of words on Birney's part, I do not understand what he means by humdrum either. What I am saying is that since we do not have evidence of strong directional selection for IQ then it must be due to drift or weak polygenic selection (unlikely due to drift because of the way human populations differ and some other stuff- see the Edge and Rosenberg,2015 I cited earlier)
But gene flow counteracts drift and selection to an extent (depending on the strength of selection) so if these 3 populations were distinct enough, it would be hard for drift or selection to lead to higher European IQ. Unless a) evolution acted faster than we think b) these populations were not that different to begin with.I just did btw. As for tedious conversation, once again if you think that about what I tell you then you will think the same about what most scientists tell you who disagree with HBD claims.Did Piffer control for population structure? (and no that is not due to big differences between populations but rather GxG, GxE interactions and LD differences )No, IQ has been selected for. Their argument is that drift is unlikely to lead to big differences on IQ.Related to the brain?Yet you accuse me of not providing relevant arguments. Why, what is wrong with it?
Do you think valid to compare PGS across populations? Even the Cofnas paper suggested caution doing that.
Genetic clustering algorithms, implemented in programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans as a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups that do not have admixture in their recent history, where recent genetic drift is strong or that deviate in other ways from the underlying inference model. Unfortunately, such histories can be misleading. We have implemented an approach, badMIXTURE, to assess the goodness of fit of the model using the ancestry “palettes” estimated by CHROMOPAINTER and apply it to both simulated data and real case studies. Combining these complementary analyses with additional methods that are designed to test specific hypotheses allows a richer and more robust analysis of recent demographic history.I will look up studies on Middle Easterners or other intermediate populations and let you know. However, in all honesty, that paper has it wrong to an extent. They are supposed to be between Europeans and Africans not between Africans and East Asians. But my point was that by finding similar studies it is possible to test if Templeton is right or wrong for example.Not always. https://www.biorxiv.org/content/10.1101/773663v2
Source populations for an admixed population can possess distinct patterns of genotype and phenotype at the beginning of the admixture process. Such differences are sometimes taken to serve as markers of ancestry---that is, phenotypes that are initially associated with the ancestral background in one source population are taken to reflect ancestry in that population. Examples exist, however, in which genotypes or phenotypes initially associated with ancestry in one source population have decoupled from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. We develop a mechanistic model for describing the joint dynamics of admixture levels and phenotype distributions in an admixed population. The approach includes a quantitative-genetic model that relates a phenotype to underlying loci that affect its trait value. We consider three forms of mating. First, individuals might assort in a manner that is independent of the overall genetic admixture level. Second, individuals might assort by a quantitative phenotype that is initially correlated with the genetic admixture level. Third, individuals might assort by the genetic admixture level itself. Under the model, we explore the relationship between genetic admixture level and phenotype over time, studying the effect on this relationship of the genetic architecture of the phenotype. We find that the decoupling of genetic ancestry and phenotype can occur surprisingly quickly, especially if the phenotype is driven by a small number of loci. We also find that positive assortative mating attenuates the process of dissociation in relation to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype. The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might be a reliable proxy for ancestry for only a short time, especially if the trait is determined by relatively few loci. The results are potentially relevant in admixed human populations, in which phenotypes that have a perceived correlation with ancestry might have social significance as ancestry markers, despite declining correlations with ancestry over time.
Arbitrary but sure I can agree on that. Groups are not necessarily races though, unless you use race differently than I do.Race is a stronger term than phenotypic differences in those traits, is all I am saying.Are you sure we are talking about the same person?
Ad hominems are not an argument (and using them is a tell that you don’t have a real argument). How about engaging with what he has actually said? Here is a link to his gene flow post (again): https://westhunt.wordpress.com/2019/01/07/gene-flow/
How about refuting it there? If he won’t post your response then post it here and we can discuss whether he is being reasonable or not.
What does that even mean? They are examples of overall genomic differentiation. How is that not informative?
(If this is typical of your field I am really glad I don’t have to read anthropology papers)
I thought you were just arguing that those two were synonymous? What really matters for race is the genetic ancestry, but the geographic ancestry serves as a decent proxy.
And how is your last sentence even relevant to this issue?
Don’t let the perfect be the enemy of the good. I thought you had agreed to work with Africans, East Asians, and Europeans as groups? Let’s do that–which would be k=3.
I don’t see how that is relevant. If you are going to endlessly spam papers and abstracts of doubtful relevance then make clear the point you have in mind.
I am going to file that away in the list of epic quotes from Anti-HBD. Yes, always. Genotype may not be completely determinative of phenotype, but it is always related. Or perhaps you would like it better if I said 99.9% percent of the time or some such? If so, give one concrete example where it is not related.
Please elaborate on how you think that paper supports your point. I am pretty sure it does not say what you think it says.
How so? Your vagueness is tedious. Though it does make a good tell for when you think you are getting into deep water.
Perhaps you failed to notice the “…” in my statement? I was not limiting myself to just those traits.
You might want to spend some time learning about this fallacy: https://en.wikipedia.org/wiki/No_true_Scotsman
Yes. As I asked in an earlier comment, how about showing me what he has to say about genetics and group differences in IQ (or height)? Surely he would be vigorously denouncing those ideas if they were untrue? And in peer reviewed research papers, not tweets.
P.S. Please respond to my PCA points. It is clear overplotting matters (and it has been 9 days since I made that point in comment 97). Admit it. And admit what that does to your clines vs. clusters argument in the PCA plot you provided. Your failure to do this is conclusive evidence of your insincerity as far as I am concerned. Stop wasting my time.
https://www.cell.com/cell/fulltext/S0092-8674(20)30059-3
Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.Most markers are neutral, is what I mean.I was mostly thinking about the markers mentioned above here. People from Africa can look the same and come from the same place but can be as genetically different as a European and an East Asian or more.
The Melanesian case was a bad example indeed.Yeah, all right I was honestly curious as to what led you choose these groups, hence my earlier question.You are being obtuse. You know in what context I mentioned it. Seeing someone is black can often be uniformative of his genetic ancestry.
That paper suggests that after a while you can not take phenotypic cues and make statements about one's ancestry or race.How so?Find me a taxonomist that does not equate race with subspecies.https://twitter.com/Graham_Coop/status/1137485922876809216
As for papers, here is one about STRUCTURE for example: https://www.genetics.org/content/210/1/33
specially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations.
If you have read his notes for example, you would see that he clearely states there is not right choice of K. You want me to respond about the PCA stuff, and I think you are correct that overplotting was the issue with the ones I cited (they apparently emphasized local relationships more than global ones hence the clinal result among the issues you brought up), can you now answer my question of a study that tested for the optimal number of K in humans ?I told you to wait while I was doing some research. Having done it, yes you are correct as I said above.
What genuinely interests me now is how this PCA distribution fits with population genetic and demographic models.
How about refuting it there? If he won't post your response then post it here and we can discuss whether he is being reasonable or not.What does that even mean? They are examples of overall genomic differentiation. How is that not informative?
(If this is typical of your field I am really glad I don't have to read anthropology papers)I thought you were just arguing that those two were synonymous? What really matters for race is the genetic ancestry, but the geographic ancestry serves as a decent proxy.
And how is your last sentence even relevant to this issue?Don't let the perfect be the enemy of the good. I thought you had agreed to work with Africans, East Asians, and Europeans as groups? Let's do that--which would be k=3.I don't see how that is relevant. If you are going to endlessly spam papers and abstracts of doubtful relevance then make clear the point you have in mind.I am going to file that away in the list of epic quotes from Anti-HBD. Yes, always. Genotype may not be completely determinative of phenotype, but it is always related. Or perhaps you would like it better if I said 99.9% percent of the time or some such? If so, give one concrete example where it is not related.
Please elaborate on how you think that paper supports your point. I am pretty sure it does not say what you think it says.How so? Your vagueness is tedious. Though it does make a good tell for when you think you are getting into deep water.
Perhaps you failed to notice the "..." in my statement? I was not limiting myself to just those traits.
You might want to spend some time learning about this fallacy: https://en.wikipedia.org/wiki/No_true_ScotsmanYes. As I asked in an earlier comment, how about showing me what he has to say about genetics and group differences in IQ (or height)? Surely he would be vigorously denouncing those ideas if they were untrue? And in peer reviewed research papers, not tweets.
P.S. Please respond to my PCA points. It is clear overplotting matters (and it has been 9 days since I made that point in comment 97). Admit it. And admit what that does to your clines vs. clusters argument in the PCA plot you provided. Your failure to do this is conclusive evidence of your insincerity as far as I am concerned. Stop wasting my time.
Well, that does not make sense to me. People must have mixed during the Ice Age and considerably so, given that it has been found that even Africans have a significant Neanderthal component ( significant as in above 0.3%, most populations have only about 1 or 2%)
https://www.cell.com/cell/fulltext/S0092-8674(20)30059-3
Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.
Most markers are neutral, is what I mean.
I was mostly thinking about the markers mentioned above here. People from Africa can look the same and come from the same place but can be as genetically different as a European and an East Asian or more.
The Melanesian case was a bad example indeed.
Yeah, all right I was honestly curious as to what led you choose these groups, hence my earlier question.
You are being obtuse. You know in what context I mentioned it. Seeing someone is black can often be uniformative of his genetic ancestry.
That paper suggests that after a while you can not take phenotypic cues and make statements about one’s ancestry or race.
How so?
Find me a taxonomist that does not equate race with subspecies.
As for papers, here is one about STRUCTURE for example: https://www.genetics.org/content/210/1/33
specially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations.
If you have read his notes for example, you would see that he clearely states there is not right choice of K. You want me to respond about the PCA stuff, and I think you are correct that overplotting was the issue with the ones I cited (they apparently emphasized local relationships more than global ones hence the clinal result among the issues you brought up), can you now answer my question of a study that tested for the optimal number of K in humans ?
I told you to wait while I was doing some research. Having done it, yes you are correct as I said above.
What genuinely interests me now is how this PCA distribution fits with population genetic and demographic models.
https://www.businessinsider.com/four-neighboring-african-tribes-are-more-genetically-different-than-ronald-reagan-and-mao-zedong-2014-2The optimal number will depend on the specific populations being examined and the purposes of the clustering. Race (ancestry, etc.) is hierarchical. Appeal to unresolvable lumper/splitter questions is a waste of time and a favorite diversionary tactic of people like you.There was not much context there. Let's give the full quote from my comment.If you are going to give an absolutist two word statement like that don't expect me to magically figure out which contexts you do and do not consider applicable. Say what you mean. Stop with the vagueness. Try that now. What is the case where your "Not always" statement is true? Are you trying to say that different genotypes can cause similar phenotypes (e.g. black skin color)? That is a very different thing than saying phenotype is unrelated to genotype. Your combination of vagueness and shifting (and unusual) definitions is generally a tell for someone not interested in having a sincere discussion.And the other 99.99% of people in the world?The tweet you linked says nothing direct about that. I think you just proved my point. Thanks.Yes, you told me that over and over while writing long comments about other things and not responding to my point. For 9 days. So what exactly am I right about? If you are sincere can you please be specific! Which of the following points do you and don't you agree with?
- Your PCA plots are subject to severe overplotting.
- That overplotting obscures the relative number of peoples in the clusters vs the clinal regions.
- Given that and the information we have about sample sizes it is clear that there are many more people in the seemingly small clusters than in the more diffuse clinal regions.
- Given that, it is clear that you have been overstating the importance of clines vs. clusters. For example, this sample comment of yours: "I showed you that it is clines rather than clusters."
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3643793
Do you agree that statement was incorrect?
I choose Africans, East Asians, and Europeans as my base groups because that is quite clearly indicated by the PCA plots (this is obvious to you, right?). Why that is so is an interesting question (and I think has interesting implications for your contention about Middle Easterners), but is not what I want to talk about here.1. Covered above.
2. I call them races because that is the historical usage. As far as the subspecies equivalence, that seems like a fairly recent notion courtesy of obfuscators like you. I don't really care what we call them. If you are so traumatized by my usage of race (which I believe is in line with how it has been used for centuries) then how about we just call them "ancestral populations"? I really don't care and consider your going on about this a giant waste of time.Of course they don't support HBD. Do you think they want to be Watsoned?Examples? I would not be quick to hang your hat on Kevin Bird's paper, BTW.There is a great deal of skepticism out there. The general technique used by the critics is one I like to call FUD (and there is some truth there, e.g. LD and cross-population use of PGS scores). But I still have yet to see a convincing explanation of why he sees such high correlations. 0.9 correlations are an awfully big coincidence. Especially when they happen over and over with different sets of SNPs. Aren't you the least little bit curious about why he keeps seeing the same result?Here is the tweet I called weak: https://twitter.com/ewanbirney/status/1221975246695063553
and the text of it: "Great work Kevin. @aylwyn_scally and myself found similar things to you - IQ genetics looks reasonable “humdrum” as quantitative trait. In addition natural selection for IQ in “Europeans” would have a complex selection pattern given the admixture of Anatolian/Yamnaya/H. gathers"
I see no evidence or argument. Hence weak. I'm not even sure I understand what your second sentence means, but I am pretty sure it is not worthwhile for this conversation. Complex seems like a meaningless adjective to apply to selection pressure. And what does it mean to call IQ genetics "humdrum"?
Do you have any idea how tedious this conversation is for me? Rather than going on and on like this how about spending that time responding to the PCA points as you keep promising to do?I don't see how that counters in any way the findings of various SNPs in IQ GWAS.Same. In particular, notice that they assume "a selectively neutral quantitative trait." That hardly holds for IQ. Or are we back to you claiming IQ has not been selected for in humans?Same. That in no way negates the SNPs having been found. It does rightly emphasize that there should be some caution in interpretation. Some of the SNPs will probably turn out to be spurious. But it is unlikely all of them will. Especially given the tendency we see of them to be related to the brain.
Rather than throwing three barely relevant papers at me, how about trying for just one straight answer?See the PCA plot statement earlier in this comment.
What makes you look insincere is assuming I am arguing in bad faith when I just post you the same arguments any anthropologist or geneticist would post you. I have stressed over and over again how there are standards used in taxonomy and genetics and you think of them as obfuscations.
Fair enough, from the paper I linked earlier: https://muse.jhu.edu/article/381884/pdf?casa_token=_09_Yn-UFgQAAAAA:rXcKpbFjoPp-HG6lguB25FMcIc62CfqkvuGqAXtQuIQsGXAxFtgFNN_CeXim-2kqfevpI71eEA
These data made it possible to see how FST played out when no one could dispute taxonomic and genetic significance. The answer surprised us. FST was pretty close to the canonical 0.15 shown so many times for human populations. In our analysis, FST was 0.12 for humans, but for humans and chimpanzees together, FST rose only to 0.18. Indeed, we found one locus, D13S122, where the size range of human and chimpanzee alleles hardly overlapped, yet FST equaled 0.15 (Figure 1). We ultimately found that the genetic and statistical model underlying FST does not fit well to human populations. Specifically, human population structure strongly biases the outcome of analyses by violating two assumptions: first, that expected genetic diversity is the same in every population; and second, that divergence between all pairs of populations is equal and independent
I am citing that in response to arguments based on Fst that Greg Cochran and other HBD people often like to make. It is not a very useful measure for human taxonomy.
I do not do it on purpose any more than you do. It probably stems that the papers I read use them differently often times than you use them here.
It is an interesting question. It would also seem as Middle Easterners are mixed with populations Europeans are not if we go strictly by PCA. However caution is needed when interpreting PCAs.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989108/
They interpreted these patterns as resulting from specific migration events, such as the migration of agriculturalists out of the Near East [1, 2, 3]. Cavalli-Sforza et al’s results have been highly influential (e.g. [4]), and controversial [5, 6, 7, 8, 9], and PCA has become heavily used in population genetics (e.g. [10, 11, 12, 13]). Despite its widespread use, the behavior of PCA with data exhibiting continuous spatial variation, such as might exist within human continental groups, has been little studied. Here, using empirical and theoretical approaches, we find that the distinctive patterns observed by Cavalli-Sforza et al resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns are not necessarily due to population movements.
On that point I think LL-CS was correct, but what I am trying to say is that position on a PCA might reflect other scenarios rather than gene flow or demographic history.
If you do not think of them are subspecies, it is easier to agree with you on what race is. Ancestral populations is not a term I have a lot of issues with.
I brought this up because you implied they do behind the lines somewhere and I have not seen evidence that is the case (with the possible exception of David Reich)
Poor choice of words on Birney’s part, I do not understand what he means by humdrum either. What I am saying is that since we do not have evidence of strong directional selection for IQ then it must be due to drift or weak polygenic selection (unlikely due to drift because of the way human populations differ and some other stuff- see the Edge and Rosenberg,2015 I cited earlier)
But gene flow counteracts drift and selection to an extent (depending on the strength of selection) so if these 3 populations were distinct enough, it would be hard for drift or selection to lead to higher European IQ. Unless a) evolution acted faster than we think b) these populations were not that different to begin with.
I just did btw. As for tedious conversation, once again if you think that about what I tell you then you will think the same about what most scientists tell you who disagree with HBD claims.
Did Piffer control for population structure? (and no that is not due to big differences between populations but rather GxG, GxE interactions and LD differences )
No, IQ has been selected for. Their argument is that drift is unlikely to lead to big differences on IQ.
Related to the brain?
Yet you accuse me of not providing relevant arguments. Why, what is wrong with it?
Do you think valid to compare PGS across populations? Even the Cofnas paper suggested caution doing that.
Appeals to ignorance and unknowability have little appeal to me.So you are at least partially agreeing with one of my two examples. And we are discussing what exactly Coop has said specifically about group differences and genetics in another exchange.
Let me be clear. I do not think either Reich or Coop support HBD in their heart or mind. However, I do think both of them realize it is at least somewhat true even if they aren't willing to say so in public. HBD is vague so let me be more precise (please consider taking this as an example to follow). Consider two statements.
1. Group differences in height are at least partly caused by group differences in height genetics.
2. Group differences in IQ are at least partly caused by group differences in IQ genetics.
I think they both realize 1. is true but might not (or might, I don't know) admit it in public. 2. is more complicated. I am not sure if they would even admit that to themselves. Crimestop can be a powerful force.Indeed. In fact that is a big part of the reason I find so much of our conversation tedious. I have heard most of these arguments before and find them unsatisfactory. Yet you just keep repeating them like a mantra rather than engaging with the possibility that they are inadequate.Piffer has nothing to do with the GWAS which are finding these SNPs. He is just using their results. Currently the largest IQ (well, education as a proxy) GWAS is Lee et al. 2018
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393768/
Your attempt to use Piffer to rebut my point is simply a demonstration of your ignorance in this area. Care to try again?See this link: https://www.unz.com/jthompson/even-more-genes-for-intelligence/
In particular, this graphic showing tissue types associated with some intelligence SNPs.
https://www.unz.com/wp-content/uploads/2017/09/Intelligent-tissues.pngI am trying to keep my comments to a manageable length. See these comments:
https://www.unz.com/isteve/adam-rutherford-how-to-fight-racism-using-science/#comment-3685680
https://www.unz.com/isteve/the-mismeasure-of-genes/#comment-3687395
https://www.unz.com/isteve/the-mismeasure-of-genes/#comment-3688303
There is something to be said for discussing a topic in the relevant thread rather than all over the place.
And notice how easy it is for me to back up my statements when you request more detail (both IQ SNPs and the brain and Kevin Bird's paper).
These data made it possible to see how FST played out when no one could dispute taxonomic and genetic significance. The answer surprised us. FST was pretty close to the canonical 0.15 shown so many times for human populations. In our analysis, FST was 0.12 for humans, but for humans and chimpanzees together, FST rose only to 0.18. Indeed, we found one locus, D13S122, where the size range of human and chimpanzee alleles hardly overlapped, yet FST equaled 0.15 (Figure 1). We ultimately found that the genetic and statistical model underlying FST does not fit well to human populations. Specifically, human population structure strongly biases the outcome of analyses by violating two assumptions: first, that expected genetic diversity is the same in every population; and second, that divergence between all pairs of populations is equal and independent
I am citing that in response to arguments based on Fst that Greg Cochran and other HBD people often like to make. It is not a very useful measure for human taxonomy.I do not do it on purpose any more than you do. It probably stems that the papers I read use them differently often times than you use them here.It is an interesting question. It would also seem as Middle Easterners are mixed with populations Europeans are not if we go strictly by PCA. However caution is needed when interpreting PCAs.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989108/
They interpreted these patterns as resulting from specific migration events, such as the migration of agriculturalists out of the Near East [1, 2, 3]. Cavalli-Sforza et al’s results have been highly influential (e.g. [4]), and controversial [5, 6, 7, 8, 9], and PCA has become heavily used in population genetics (e.g. [10, 11, 12, 13]). Despite its widespread use, the behavior of PCA with data exhibiting continuous spatial variation, such as might exist within human continental groups, has been little studied. Here, using empirical and theoretical approaches, we find that the distinctive patterns observed by Cavalli-Sforza et al resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns are not necessarily due to population movements.
On that point I think LL-CS was correct, but what I am trying to say is that position on a PCA might reflect other scenarios rather than gene flow or demographic history.If you do not think of them are subspecies, it is easier to agree with you on what race is. Ancestral populations is not a term I have a lot of issues with.I brought this up because you implied they do behind the lines somewhere and I have not seen evidence that is the case (with the possible exception of David Reich)Poor choice of words on Birney's part, I do not understand what he means by humdrum either. What I am saying is that since we do not have evidence of strong directional selection for IQ then it must be due to drift or weak polygenic selection (unlikely due to drift because of the way human populations differ and some other stuff- see the Edge and Rosenberg,2015 I cited earlier)
But gene flow counteracts drift and selection to an extent (depending on the strength of selection) so if these 3 populations were distinct enough, it would be hard for drift or selection to lead to higher European IQ. Unless a) evolution acted faster than we think b) these populations were not that different to begin with.I just did btw. As for tedious conversation, once again if you think that about what I tell you then you will think the same about what most scientists tell you who disagree with HBD claims.Did Piffer control for population structure? (and no that is not due to big differences between populations but rather GxG, GxE interactions and LD differences )No, IQ has been selected for. Their argument is that drift is unlikely to lead to big differences on IQ.Related to the brain?Yet you accuse me of not providing relevant arguments. Why, what is wrong with it?
Do you think valid to compare PGS across populations? Even the Cofnas paper suggested caution doing that.
All you do is saying arguments people make are irrelevant but I would be more convinced if you offered me counter arguments supported by papers instead.
Res has done that for example, much easier to see the other person's point that way.
https://www.cell.com/cell/fulltext/S0092-8674(20)30059-3
Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.Most markers are neutral, is what I mean.I was mostly thinking about the markers mentioned above here. People from Africa can look the same and come from the same place but can be as genetically different as a European and an East Asian or more.
The Melanesian case was a bad example indeed.Yeah, all right I was honestly curious as to what led you choose these groups, hence my earlier question.You are being obtuse. You know in what context I mentioned it. Seeing someone is black can often be uniformative of his genetic ancestry.
That paper suggests that after a while you can not take phenotypic cues and make statements about one's ancestry or race.How so?Find me a taxonomist that does not equate race with subspecies.https://twitter.com/Graham_Coop/status/1137485922876809216
As for papers, here is one about STRUCTURE for example: https://www.genetics.org/content/210/1/33
specially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations.
If you have read his notes for example, you would see that he clearely states there is not right choice of K. You want me to respond about the PCA stuff, and I think you are correct that overplotting was the issue with the ones I cited (they apparently emphasized local relationships more than global ones hence the clinal result among the issues you brought up), can you now answer my question of a study that tested for the optimal number of K in humans ?I told you to wait while I was doing some research. Having done it, yes you are correct as I said above.
What genuinely interests me now is how this PCA distribution fits with population genetic and demographic models.
The argument is simple. Current observed Fsts are large enough that gene flow cannot have been as significant as you (and others) seem to think. Seems like a great example of a beautiful (and cherished by some) theory slain by an ugly fact. Reality >> theory.
Evidence? Are you referring to genotype or observable phenotype? How many markers have to be non-neutral for them to matter? Does a marker being non-neutral make it any less of a marker?
Evidence? Lots of people say things like this, but is it really true? How alike do those diverse Africans truly look? And how genetically different are they really? For example, here is an article that asserts your point, but it turns out they are only looking at mtDNA split times, not actual genetic differences.
https://www.businessinsider.com/four-neighboring-african-tribes-are-more-genetically-different-than-ronald-reagan-and-mao-zedong-2014-2
The optimal number will depend on the specific populations being examined and the purposes of the clustering. Race (ancestry, etc.) is hierarchical. Appeal to unresolvable lumper/splitter questions is a waste of time and a favorite diversionary tactic of people like you.
There was not much context there. Let’s give the full quote from my comment.
If you are going to give an absolutist two word statement like that don’t expect me to magically figure out which contexts you do and do not consider applicable. Say what you mean. Stop with the vagueness. Try that now. What is the case where your “Not always” statement is true? Are you trying to say that different genotypes can cause similar phenotypes (e.g. black skin color)? That is a very different thing than saying phenotype is unrelated to genotype. Your combination of vagueness and shifting (and unusual) definitions is generally a tell for someone not interested in having a sincere discussion.
And the other 99.99% of people in the world?
The tweet you linked says nothing direct about that. I think you just proved my point. Thanks.
Yes, you told me that over and over while writing long comments about other things and not responding to my point. For 9 days. So what exactly am I right about? If you are sincere can you please be specific! Which of the following points do you and don’t you agree with?
– Your PCA plots are subject to severe overplotting.
– That overplotting obscures the relative number of peoples in the clusters vs the clinal regions.
– Given that and the information we have about sample sizes it is clear that there are many more people in the seemingly small clusters than in the more diffuse clinal regions.
– Given that, it is clear that you have been overstating the importance of clines vs. clusters. For example, this sample comment of yours: “I showed you that it is clines rather than clusters.”
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3643793
Do you agree that statement was incorrect?
https://twitter.com/sillyolyou/status/1224661458442735616
https://twitter.com/sillyolyou/status/1224712062863118336
https://twitter.com/sillyolyou/status/1224711073799995398
We can see Greg Cochran is wrong here.Genotype. No it does not make it any less of a marker just that few of those actually exist: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000500
Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.https://twitter.com/pontus_skoglund/status/783670519619026944
Did you read the recent paper on Africa by Lipson et al?
(also found this: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1679-2)
Not read it in detail yet, but interestingly seems to make your point about Middle Easterners on the PCA, among talking about African variation.Fair enough, but that is more like race as population than race as subspecies.I often type fast and perhaps understand some terms in different context than you. I am not doing it on purpose or in bad faith, or else I would not be having this discussion with you. Are you also replying in good faith?Why would it matter?Why would he tweet those statements if he was not opposed to HBD ideas?Was on and off and doing research about your point. I did show your argument to a geneticist who was dismissive of it but I think you have a point that
Your PCA plots are subject to severe overplotting.
–Yes agreed. And emphasizes more local relationships than global ones.Agreed but the question is how to objectively divide them.Seems like it is both clines and clusters based on your argument though I am waiting to hear back from a geneticist about it.Yes.
https://twitter.com/sillyolyou/status/1224762005782958082
These data made it possible to see how FST played out when no one could dispute taxonomic and genetic significance. The answer surprised us. FST was pretty close to the canonical 0.15 shown so many times for human populations. In our analysis, FST was 0.12 for humans, but for humans and chimpanzees together, FST rose only to 0.18. Indeed, we found one locus, D13S122, where the size range of human and chimpanzee alleles hardly overlapped, yet FST equaled 0.15 (Figure 1). We ultimately found that the genetic and statistical model underlying FST does not fit well to human populations. Specifically, human population structure strongly biases the outcome of analyses by violating two assumptions: first, that expected genetic diversity is the same in every population; and second, that divergence between all pairs of populations is equal and independent
I am citing that in response to arguments based on Fst that Greg Cochran and other HBD people often like to make. It is not a very useful measure for human taxonomy.I do not do it on purpose any more than you do. It probably stems that the papers I read use them differently often times than you use them here.It is an interesting question. It would also seem as Middle Easterners are mixed with populations Europeans are not if we go strictly by PCA. However caution is needed when interpreting PCAs.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989108/
They interpreted these patterns as resulting from specific migration events, such as the migration of agriculturalists out of the Near East [1, 2, 3]. Cavalli-Sforza et al’s results have been highly influential (e.g. [4]), and controversial [5, 6, 7, 8, 9], and PCA has become heavily used in population genetics (e.g. [10, 11, 12, 13]). Despite its widespread use, the behavior of PCA with data exhibiting continuous spatial variation, such as might exist within human continental groups, has been little studied. Here, using empirical and theoretical approaches, we find that the distinctive patterns observed by Cavalli-Sforza et al resemble sinusoidal mathematical artifacts that arise generally when PCA is applied to spatial data, implying that the patterns are not necessarily due to population movements.
On that point I think LL-CS was correct, but what I am trying to say is that position on a PCA might reflect other scenarios rather than gene flow or demographic history.If you do not think of them are subspecies, it is easier to agree with you on what race is. Ancestral populations is not a term I have a lot of issues with.I brought this up because you implied they do behind the lines somewhere and I have not seen evidence that is the case (with the possible exception of David Reich)Poor choice of words on Birney's part, I do not understand what he means by humdrum either. What I am saying is that since we do not have evidence of strong directional selection for IQ then it must be due to drift or weak polygenic selection (unlikely due to drift because of the way human populations differ and some other stuff- see the Edge and Rosenberg,2015 I cited earlier)
But gene flow counteracts drift and selection to an extent (depending on the strength of selection) so if these 3 populations were distinct enough, it would be hard for drift or selection to lead to higher European IQ. Unless a) evolution acted faster than we think b) these populations were not that different to begin with.I just did btw. As for tedious conversation, once again if you think that about what I tell you then you will think the same about what most scientists tell you who disagree with HBD claims.Did Piffer control for population structure? (and no that is not due to big differences between populations but rather GxG, GxE interactions and LD differences )No, IQ has been selected for. Their argument is that drift is unlikely to lead to big differences on IQ.Related to the brain?Yet you accuse me of not providing relevant arguments. Why, what is wrong with it?
Do you think valid to compare PGS across populations? Even the Cofnas paper suggested caution doing that.
Please at least consider the possibility that those arguments ARE obfuscations. If so, then my behavior is completely reasonable. And you might ponder how sincere you look viewed through that lens.
Feel free to suggest a better measure. Until then, we keep using Fst while trying to keep in mind relevant caveats.
Appeals to ignorance and unknowability have little appeal to me.
So you are at least partially agreeing with one of my two examples. And we are discussing what exactly Coop has said specifically about group differences and genetics in another exchange.
Let me be clear. I do not think either Reich or Coop support HBD in their heart or mind. However, I do think both of them realize it is at least somewhat true even if they aren’t willing to say so in public. HBD is vague so let me be more precise (please consider taking this as an example to follow). Consider two statements.
1. Group differences in height are at least partly caused by group differences in height genetics.
2. Group differences in IQ are at least partly caused by group differences in IQ genetics.
I think they both realize 1. is true but might not (or might, I don’t know) admit it in public. 2. is more complicated. I am not sure if they would even admit that to themselves. Crimestop can be a powerful force.
Indeed. In fact that is a big part of the reason I find so much of our conversation tedious. I have heard most of these arguments before and find them unsatisfactory. Yet you just keep repeating them like a mantra rather than engaging with the possibility that they are inadequate.
Piffer has nothing to do with the GWAS which are finding these SNPs. He is just using their results. Currently the largest IQ (well, education as a proxy) GWAS is Lee et al. 2018
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393768/
Your attempt to use Piffer to rebut my point is simply a demonstration of your ignorance in this area. Care to try again?
See this link: https://www.unz.com/jthompson/even-more-genes-for-intelligence/
In particular, this graphic showing tissue types associated with some intelligence SNPs.
I am trying to keep my comments to a manageable length. See these comments:
https://www.unz.com/isteve/adam-rutherford-how-to-fight-racism-using-science/#comment-3685680
https://www.unz.com/isteve/the-mismeasure-of-genes/#comment-3687395
https://www.unz.com/isteve/the-mismeasure-of-genes/#comment-3688303
There is something to be said for discussing a topic in the relevant thread rather than all over the place.
And notice how easy it is for me to back up my statements when you request more detail (both IQ SNPs and the brain and Kevin Bird’s paper).
These are the standards people use not only in anthropology but genetics. I have had conversations with geneticists, been to some seminars and read a fair amount of papers. I am not making them up.I study human evolution and like many others who do (from various fields) I am interested in evolutionary relationships of populations. A race that is defined by shared phenotype like Africans tells me little about their evolutionary history (beyond skin color or perhaps other phenotypic traits) if they do not share a genetic connection stronger than that with other populations or races as you would call them. Something that helps us understand their demographic history, detect selection etc.
I do not know if it is feasible for you or not, but that blog with the cophenetic relationship seems interesting. If his result can be replicated (I do not have the software to do so) then that is a good measure of races (even if it is k=3 like we said, means these groups have evolved in enough isolation and are sufficiently different even excluding intermediate populations)Kevin also used the Lee et al data to prove his argument.
But, let me read more about this and will get back to you. It is not my field of expertise.
https://www.businessinsider.com/four-neighboring-african-tribes-are-more-genetically-different-than-ronald-reagan-and-mao-zedong-2014-2The optimal number will depend on the specific populations being examined and the purposes of the clustering. Race (ancestry, etc.) is hierarchical. Appeal to unresolvable lumper/splitter questions is a waste of time and a favorite diversionary tactic of people like you.There was not much context there. Let's give the full quote from my comment.If you are going to give an absolutist two word statement like that don't expect me to magically figure out which contexts you do and do not consider applicable. Say what you mean. Stop with the vagueness. Try that now. What is the case where your "Not always" statement is true? Are you trying to say that different genotypes can cause similar phenotypes (e.g. black skin color)? That is a very different thing than saying phenotype is unrelated to genotype. Your combination of vagueness and shifting (and unusual) definitions is generally a tell for someone not interested in having a sincere discussion.And the other 99.99% of people in the world?The tweet you linked says nothing direct about that. I think you just proved my point. Thanks.Yes, you told me that over and over while writing long comments about other things and not responding to my point. For 9 days. So what exactly am I right about? If you are sincere can you please be specific! Which of the following points do you and don't you agree with?
- Your PCA plots are subject to severe overplotting.
- That overplotting obscures the relative number of peoples in the clusters vs the clinal regions.
- Given that and the information we have about sample sizes it is clear that there are many more people in the seemingly small clusters than in the more diffuse clinal regions.
- Given that, it is clear that you have been overstating the importance of clines vs. clusters. For example, this sample comment of yours: "I showed you that it is clines rather than clusters."
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3643793
Do you agree that statement was incorrect?
These Fst values do not mean low gene flow or high differentiation. See the tweets below (particularly the first 2):
We can see Greg Cochran is wrong here.
Genotype. No it does not make it any less of a marker just that few of those actually exist: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000500
Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.
Did you read the recent paper on Africa by Lipson et al?
(also found this: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1679-2)
Not read it in detail yet, but interestingly seems to make your point about Middle Easterners on the PCA, among talking about African variation.
Fair enough, but that is more like race as population than race as subspecies.
I often type fast and perhaps understand some terms in different context than you. I am not doing it on purpose or in bad faith, or else I would not be having this discussion with you. Are you also replying in good faith?
Why would it matter?
Why would he tweet those statements if he was not opposed to HBD ideas?
Was on and off and doing research about your point. I did show your argument to a geneticist who was dismissive of it but I think you have a point that
Your PCA plots are subject to severe overplotting.
–
Yes agreed. And emphasizes more local relationships than global ones.
Agreed but the question is how to objectively divide them.
Seems like it is both clines and clusters based on your argument though I am waiting to hear back from a geneticist about it.
Yes.
This is the kind of thing which makes you seem insincere (or would it be more charitable to say ignorant of basic logic? you can decide)Notice their focus on "fixed." That is one of the standbys of race deniers. That by no means refutes the reality of large and systematic differences in genomes across races (shown clearly by PCA plots).
If you are sincere I will say again. You need to make an effort to read things more carefully. That was a great example of an obfuscatory argument (along the lines of Lewontin's Fallacy). You take a very specific true statement like "there are surprisingly few fixed or nearly fixed differences between human populations" and attempt to use it to assert things like "race does not exist."
If you have a set of 20 SNPs which are all 90/10 distributed systematically between different populations then even though no one of those serves as a definitive marker they all serve as markers which in aggregate can distinguish the groups (this is what we see in the PCA plots).Perhaps type less more slowly? There is a reason you have been accused of Gish Galloping.
I have been very specific in my responses to you and I believe my presentation has been consistent. In particular, notice my use of clarifying questions (rather than making assumptions about what you think/say). Is there something in particular that you think demonstrates my bad faith. (I will note, tu quoque is considered a fallacy for a reason https://en.wikipedia.org/wiki/Tu_quoque) Vague (or implied) accusations are much less compelling than specific. Here are some specific reasons I think you are acting in bad faith.
- Your vagueness and shifting definitions (as I have said more than once).
- Your refusal to acknowledge good opposing points. You have been getting better about this, but still need to be more clear about what shared understanding there is.
- Logical fallacies. False dichotomies are the most common. With appeals to authorities making an appearance. You seem to recently be engaging in tu quoque by questioning my good faith. We see No True Scotsman (no true marker). And the Continuum fallacy https://en.wikipedia.org/wiki/Continuum_fallacy (e.g. clines disprove clusters) has been a mainstay of yours.Are you seriously telling me that the way 99.99% of the people in the world use a word does not matter in terms of how we are to interpret it? If so, that goes into my list of epic Anti-HBD quotes.Please work on your reading comprehension. I was quite clear about agreeing that Coop is opposed to HBD ideas. My issue is whether he ever makes points which actually demonstrate they are wrong. He usually reconciles this by making a related point with an implied argument that a particular HBD assertion (how about we be more specific and talk about particular assertions rather than "HBD"?) is wrong, while never actually engaging with the substance of a given assertion. Your tweet was a perfect example of that. Which was why I said (and continue to say) it proves my point.Dismissive how? Perhaps you could pass along the actual reply? One of the reasons I engage with you is that if you are actually sincere and have an open mind you will eventually figure out that "dismissing" things without actually refuting them is standard behavior for questions like this. And see just how hollow the dogma you have committed to is.How do you objectively divide red, orange, and yellow? I hope you don't apply this style of thinking to everything in life. See the Continuum fallacy comment above.This should be interesting. How about passing along their full reply? I think it would be interesting to try to interpret it myself.Thank you. That goes a long way towards making you seem sincere.
P.S. It would be helpful if you clarified where arguments are your own and where they have been supplied by someone else (e.g. the geneticist you consult). I get the sense there are some things being lost in translation.
Appeals to ignorance and unknowability have little appeal to me.So you are at least partially agreeing with one of my two examples. And we are discussing what exactly Coop has said specifically about group differences and genetics in another exchange.
Let me be clear. I do not think either Reich or Coop support HBD in their heart or mind. However, I do think both of them realize it is at least somewhat true even if they aren't willing to say so in public. HBD is vague so let me be more precise (please consider taking this as an example to follow). Consider two statements.
1. Group differences in height are at least partly caused by group differences in height genetics.
2. Group differences in IQ are at least partly caused by group differences in IQ genetics.
I think they both realize 1. is true but might not (or might, I don't know) admit it in public. 2. is more complicated. I am not sure if they would even admit that to themselves. Crimestop can be a powerful force.Indeed. In fact that is a big part of the reason I find so much of our conversation tedious. I have heard most of these arguments before and find them unsatisfactory. Yet you just keep repeating them like a mantra rather than engaging with the possibility that they are inadequate.Piffer has nothing to do with the GWAS which are finding these SNPs. He is just using their results. Currently the largest IQ (well, education as a proxy) GWAS is Lee et al. 2018
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393768/
Your attempt to use Piffer to rebut my point is simply a demonstration of your ignorance in this area. Care to try again?See this link: https://www.unz.com/jthompson/even-more-genes-for-intelligence/
In particular, this graphic showing tissue types associated with some intelligence SNPs.
https://www.unz.com/wp-content/uploads/2017/09/Intelligent-tissues.pngI am trying to keep my comments to a manageable length. See these comments:
https://www.unz.com/isteve/adam-rutherford-how-to-fight-racism-using-science/#comment-3685680
https://www.unz.com/isteve/the-mismeasure-of-genes/#comment-3687395
https://www.unz.com/isteve/the-mismeasure-of-genes/#comment-3688303
There is something to be said for discussing a topic in the relevant thread rather than all over the place.
And notice how easy it is for me to back up my statements when you request more detail (both IQ SNPs and the brain and Kevin Bird's paper).
Fair enough, but please consider the possibility that I am not doing this any more than you think the authors do.
These are the standards people use not only in anthropology but genetics. I have had conversations with geneticists, been to some seminars and read a fair amount of papers. I am not making them up.
I study human evolution and like many others who do (from various fields) I am interested in evolutionary relationships of populations. A race that is defined by shared phenotype like Africans tells me little about their evolutionary history (beyond skin color or perhaps other phenotypic traits) if they do not share a genetic connection stronger than that with other populations or races as you would call them. Something that helps us understand their demographic history, detect selection etc.
I do not know if it is feasible for you or not, but that blog with the cophenetic relationship seems interesting. If his result can be replicated (I do not have the software to do so) then that is a good measure of races (even if it is k=3 like we said, means these groups have evolved in enough isolation and are sufficiently different even excluding intermediate populations)
Kevin also used the Lee et al data to prove his argument.
But, let me read more about this and will get back to you. It is not my field of expertise.
https://pumpkinperson.com/2019/05/28/genetic-distance-the-cophenetic-correlation/Yes. Bird seems to agree that the Lee et al. data and analysis are good. Which supports my original point. From comment 110: "How can you say “they have not been found and are unlikely to” given the progress we have seen in GWAS for these traits?"
So your argument quoted above is an affirmation of my point, not a rebuttal. Care to try again one more time? Or perhaps it would be better for you to stop digging this particular hole deeper?
Why did you never reply with an argument against that clines paper that was cited to you in the Thompson thread?
All you do is saying arguments people make are irrelevant but I would be more convinced if you offered me counter arguments supported by papers instead.
Res has done that for example, much easier to see the other person’s point that way.
https://www.businessinsider.com/four-neighboring-african-tribes-are-more-genetically-different-than-ronald-reagan-and-mao-zedong-2014-2The optimal number will depend on the specific populations being examined and the purposes of the clustering. Race (ancestry, etc.) is hierarchical. Appeal to unresolvable lumper/splitter questions is a waste of time and a favorite diversionary tactic of people like you.There was not much context there. Let's give the full quote from my comment.If you are going to give an absolutist two word statement like that don't expect me to magically figure out which contexts you do and do not consider applicable. Say what you mean. Stop with the vagueness. Try that now. What is the case where your "Not always" statement is true? Are you trying to say that different genotypes can cause similar phenotypes (e.g. black skin color)? That is a very different thing than saying phenotype is unrelated to genotype. Your combination of vagueness and shifting (and unusual) definitions is generally a tell for someone not interested in having a sincere discussion.And the other 99.99% of people in the world?The tweet you linked says nothing direct about that. I think you just proved my point. Thanks.Yes, you told me that over and over while writing long comments about other things and not responding to my point. For 9 days. So what exactly am I right about? If you are sincere can you please be specific! Which of the following points do you and don't you agree with?
- Your PCA plots are subject to severe overplotting.
- That overplotting obscures the relative number of peoples in the clusters vs the clinal regions.
- Given that and the information we have about sample sizes it is clear that there are many more people in the seemingly small clusters than in the more diffuse clinal regions.
- Given that, it is clear that you have been overstating the importance of clines vs. clusters. For example, this sample comment of yours: "I showed you that it is clines rather than clusters."
https://www.unz.com/jthompson/explaining-race-and-genetics-no-need-to-despair/?showcomments#comment-3643793
Do you agree that statement was incorrect?
I do not want to spam but this tweet is exactly why I think Fst comparisons are dubious.
These are the standards people use not only in anthropology but genetics. I have had conversations with geneticists, been to some seminars and read a fair amount of papers. I am not making them up.I study human evolution and like many others who do (from various fields) I am interested in evolutionary relationships of populations. A race that is defined by shared phenotype like Africans tells me little about their evolutionary history (beyond skin color or perhaps other phenotypic traits) if they do not share a genetic connection stronger than that with other populations or races as you would call them. Something that helps us understand their demographic history, detect selection etc.
I do not know if it is feasible for you or not, but that blog with the cophenetic relationship seems interesting. If his result can be replicated (I do not have the software to do so) then that is a good measure of races (even if it is k=3 like we said, means these groups have evolved in enough isolation and are sufficiently different even excluding intermediate populations)Kevin also used the Lee et al data to prove his argument.
But, let me read more about this and will get back to you. It is not my field of expertise.
Still not getting it after all this time. Whether you’re lying or stupid, either way is a waste of time.
You never make any arguments, only hand-waving.
Yes I know you will tell me something about shared ancestry or something but the fact remains, San and Yoruba or Somalis do not share any more recent ancestry than Somali populations and Europeans or even Yoruba and Europeans.
You never make any arguments, only hand-waving.
You never make any arguments, only hand-waving.
So you know you were making a strawman argument? What the hell is wrong with you? And then you change the subject to a new lie (which has already been addressed ad nauseam) when called on it?
You talked about ancestry before and I think I also asked you: Do Southern Europeans share more ancestry with Middle Easterners than Northern Europeans? If you replied and I missed it then my bad, but I do not think so.
Going by k=3 that I agreed with @res, then the shared ancestry stuff is still about quantity of a shared genomic component, not that one population has ancestry from a past population the other one does not (ie East Asians and Europeans share some recent genetic ancestry)
Exceptions exist at k=5 (Aboriginal Australians being one) but that is the last 10.000 years or so. There was much genetic exchange before that period as ancient DNA has shown even if you disagree with Templeton's analysis. As you might know, even Native Americans share ancestry with Europeans (among many others) via the Ancient North Eurasian population.
https://twitter.com/sillyolyou/status/1224661458442735616
https://twitter.com/sillyolyou/status/1224712062863118336
https://twitter.com/sillyolyou/status/1224711073799995398
We can see Greg Cochran is wrong here.Genotype. No it does not make it any less of a marker just that few of those actually exist: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000500
Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.https://twitter.com/pontus_skoglund/status/783670519619026944
Did you read the recent paper on Africa by Lipson et al?
(also found this: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1679-2)
Not read it in detail yet, but interestingly seems to make your point about Middle Easterners on the PCA, among talking about African variation.Fair enough, but that is more like race as population than race as subspecies.I often type fast and perhaps understand some terms in different context than you. I am not doing it on purpose or in bad faith, or else I would not be having this discussion with you. Are you also replying in good faith?Why would it matter?Why would he tweet those statements if he was not opposed to HBD ideas?Was on and off and doing research about your point. I did show your argument to a geneticist who was dismissive of it but I think you have a point that
Your PCA plots are subject to severe overplotting.
–Yes agreed. And emphasizes more local relationships than global ones.Agreed but the question is how to objectively divide them.Seems like it is both clines and clusters based on your argument though I am waiting to hear back from a geneticist about it.Yes.
It looks like Cochran was wrong in using the coyote example as an analogy. I think you need to learn a bit more about how and why (and when, i.e. not in this case) refuting a single example implies that the entire point is refuted.
This is the kind of thing which makes you seem insincere (or would it be more charitable to say ignorant of basic logic? you can decide)
Notice their focus on “fixed.” That is one of the standbys of race deniers. That by no means refutes the reality of large and systematic differences in genomes across races (shown clearly by PCA plots).
If you are sincere I will say again. You need to make an effort to read things more carefully. That was a great example of an obfuscatory argument (along the lines of Lewontin’s Fallacy). You take a very specific true statement like “there are surprisingly few fixed or nearly fixed differences between human populations” and attempt to use it to assert things like “race does not exist.”
If you have a set of 20 SNPs which are all 90/10 distributed systematically between different populations then even though no one of those serves as a definitive marker they all serve as markers which in aggregate can distinguish the groups (this is what we see in the PCA plots).
Perhaps type less more slowly? There is a reason you have been accused of Gish Galloping.
I have been very specific in my responses to you and I believe my presentation has been consistent. In particular, notice my use of clarifying questions (rather than making assumptions about what you think/say). Is there something in particular that you think demonstrates my bad faith. (I will note, tu quoque is considered a fallacy for a reason https://en.wikipedia.org/wiki/Tu_quoque) Vague (or implied) accusations are much less compelling than specific. Here are some specific reasons I think you are acting in bad faith.
– Your vagueness and shifting definitions (as I have said more than once).
– Your refusal to acknowledge good opposing points. You have been getting better about this, but still need to be more clear about what shared understanding there is.
– Logical fallacies. False dichotomies are the most common. With appeals to authorities making an appearance. You seem to recently be engaging in tu quoque by questioning my good faith. We see No True Scotsman (no true marker). And the Continuum fallacy https://en.wikipedia.org/wiki/Continuum_fallacy (e.g. clines disprove clusters) has been a mainstay of yours.
Are you seriously telling me that the way 99.99% of the people in the world use a word does not matter in terms of how we are to interpret it? If so, that goes into my list of epic Anti-HBD quotes.
Please work on your reading comprehension. I was quite clear about agreeing that Coop is opposed to HBD ideas. My issue is whether he ever makes points which actually demonstrate they are wrong. He usually reconciles this by making a related point with an implied argument that a particular HBD assertion (how about we be more specific and talk about particular assertions rather than “HBD”?) is wrong, while never actually engaging with the substance of a given assertion. Your tweet was a perfect example of that. Which was why I said (and continue to say) it proves my point.
Dismissive how? Perhaps you could pass along the actual reply? One of the reasons I engage with you is that if you are actually sincere and have an open mind you will eventually figure out that “dismissing” things without actually refuting them is standard behavior for questions like this. And see just how hollow the dogma you have committed to is.
How do you objectively divide red, orange, and yellow? I hope you don’t apply this style of thinking to everything in life. See the Continuum fallacy comment above.
This should be interesting. How about passing along their full reply? I think it would be interesting to try to interpret it myself.
Thank you. That goes a long way towards making you seem sincere.
P.S. It would be helpful if you clarified where arguments are your own and where they have been supplied by someone else (e.g. the geneticist you consult). I get the sense there are some things being lost in translation.
https://twitter.com/sillyolyou/status/1224762005782958082Apologies for not replying yet on Kevin Bird's paper, as I said it is not my field of expertise and I need time to hear back from some people I asked on this. I am willing to consider that he might be wrong to an extent in some of his arguments as I can not judge for myself.If you define race that way then it is not much different from the concept of population though, is it? Not subspecies as @Theodore would have it for example.Population structure is not random, that is true. But even if a PCA overplots intermediate populations, why would you necessarily think that they are the admixed ones, instead of just giving ancestry to both populations on its extremities? Anyways, going back at K=3. PCA shows these 3 populations distinct yes, but that does not mean large differences when actually calculating their genetic distances. Moderate differentiation at best. Systematic sure, but multivariate methods usually show correlations no matter how weak they are.
https://pbs.twimg.com/media/D7zytYJWwAAJP4D?format=png&name=smallSometimes I am not understanding what you are referring to. It is not vagueness on purpose. But fair enough, I will try to be more specific.I think part of it is that I think races as formal taxonomic categories and try to use the standards used in systematics and physical anthropology to examine your argument. On the other hand, you seem to be using race as being closer to population, but correct me if I am wrong here. I can get more easily behind the 2nd concept.
I will try to give more consideration to your point of view, in any case.The Continuum fallacy is interesting, though there are arguements against it being a fallacy. The issue with clines is that it does not allow for an objective partition of the variation which is an issue for anyone interested in human taxonomy and also makes it hard to distinguish between clusters when sampling many populations. It is why I brought it up earlier, but will not expand more on it as we are talking about k=3 here. I can even accept that you can divide African populations in many clusters and still have races in humans, just more in Africa. However, do not HBDers also engage in No True Scotsman? I have seen debates on the sickle cell allele, (Greeks have it for example and the response is usually something along but most Europeans dont!) or admixture ( recent East Asian admixture in Russians, Finns, Polish and many other Eastern Europeans, African admixture in southern Europeans - counter argument is but most Europeans do not! -who is most here?)I am not saying the above examples disprove race, but just to give you an idea that it is not a fallacy used by anti-hereditarians only.You are welcome, but my point was that expert opinion matters in those issues, why would it not?Fair enough, but I know what I am talking about when I say he has very good arguments about why specific hereditarian claims, including human races do not exist. Alas, only by asking him you can really know so let us agree (being unable to cite specific technical statements of his here) that it is possible you are correct regarding your opinion on him.Not sure how to pass along the actual reply but in any case, the statement was mostly along these lines: First of all, had races existed then we would expect that the genetic distance between any two populations would be proportional to the time at which they split from a common ancestral population in the tree.
Regarding specifically the clines vs clusters issue, since clusters account for only 2% of the variation and clines for most of the variation clusters are taxonomically meaningless. Its all in that paper that he sent me really, what I also think to be the strongest case for clines vs clusters or both clines and clustures (open to the third possibility)https://serval.unil.ch/resource/serval:BIB_B0CA510362E4.P001/REF.pdf
An even more striking feature in the microsatellite data is that geographic distance from East Africa (the probable cradle of anatomically modern humans (e.g. Refs [19,20]) explains an impressive 85% of the smooth decrease in gene diversity (Hs) within human populations [10,12,13] (Figure 1b and Box 1 Figure Ib). Perhaps even more remarkably, similar clinal patterns can be recovered for variation in human craniometric measurements [21] and even the gut bacterium Helicobacter pylori, suggesting that this species has been commensal with human populations since our initial exit from Africa [13]. In each case, no step decrease(s) in genetic diversity were found that could be interpreted as evidence for genetic discontinuities, even at continental boundaries.Are there papers that contradict that last sentence? Again, honestly asking, I just do not know of any. In particular see figure 1 and their statement on the 2nd page on Native Americans and how that example can work for any clusters or continental populations. As mentioned in the main text (Figure 1b), >75% ofthe total variance of pairwise FST can be captured by geographic distance alone. Adding information on genetic clusters to this model captures only an extra 2% of the varianceWhy can then we objectively divide chimpanzees or other species? (Not all, -I know- for the same reasons as humans often)If the paper I posted earlier does not satisfy you then I will.As requested, I received help with the Handley et al,2007 paper I cited above. Rest are mine.
What exactly is the new lie and the strawman argument? Maybe Somalis was an unfortunate example due to them having considerable West Eurasian ancestry but the rest of my argument stands.
You talked about ancestry before and I think I also asked you: Do Southern Europeans share more ancestry with Middle Easterners than Northern Europeans? If you replied and I missed it then my bad, but I do not think so.
Going by k=3 that I agreed with , then the shared ancestry stuff is still about quantity of a shared genomic component, not that one population has ancestry from a past population the other one does not (ie East Asians and Europeans share some recent genetic ancestry)
Exceptions exist at k=5 (Aboriginal Australians being one) but that is the last 10.000 years or so. There was much genetic exchange before that period as ancient DNA has shown even if you disagree with Templeton’s analysis. As you might know, even Native Americans share ancestry with Europeans (among many others) via the Ancient North Eurasian population.
This is the kind of thing which makes you seem insincere (or would it be more charitable to say ignorant of basic logic? you can decide)Notice their focus on "fixed." That is one of the standbys of race deniers. That by no means refutes the reality of large and systematic differences in genomes across races (shown clearly by PCA plots).
If you are sincere I will say again. You need to make an effort to read things more carefully. That was a great example of an obfuscatory argument (along the lines of Lewontin's Fallacy). You take a very specific true statement like "there are surprisingly few fixed or nearly fixed differences between human populations" and attempt to use it to assert things like "race does not exist."
If you have a set of 20 SNPs which are all 90/10 distributed systematically between different populations then even though no one of those serves as a definitive marker they all serve as markers which in aggregate can distinguish the groups (this is what we see in the PCA plots).Perhaps type less more slowly? There is a reason you have been accused of Gish Galloping.
I have been very specific in my responses to you and I believe my presentation has been consistent. In particular, notice my use of clarifying questions (rather than making assumptions about what you think/say). Is there something in particular that you think demonstrates my bad faith. (I will note, tu quoque is considered a fallacy for a reason https://en.wikipedia.org/wiki/Tu_quoque) Vague (or implied) accusations are much less compelling than specific. Here are some specific reasons I think you are acting in bad faith.
- Your vagueness and shifting definitions (as I have said more than once).
- Your refusal to acknowledge good opposing points. You have been getting better about this, but still need to be more clear about what shared understanding there is.
- Logical fallacies. False dichotomies are the most common. With appeals to authorities making an appearance. You seem to recently be engaging in tu quoque by questioning my good faith. We see No True Scotsman (no true marker). And the Continuum fallacy https://en.wikipedia.org/wiki/Continuum_fallacy (e.g. clines disprove clusters) has been a mainstay of yours.Are you seriously telling me that the way 99.99% of the people in the world use a word does not matter in terms of how we are to interpret it? If so, that goes into my list of epic Anti-HBD quotes.Please work on your reading comprehension. I was quite clear about agreeing that Coop is opposed to HBD ideas. My issue is whether he ever makes points which actually demonstrate they are wrong. He usually reconciles this by making a related point with an implied argument that a particular HBD assertion (how about we be more specific and talk about particular assertions rather than "HBD"?) is wrong, while never actually engaging with the substance of a given assertion. Your tweet was a perfect example of that. Which was why I said (and continue to say) it proves my point.Dismissive how? Perhaps you could pass along the actual reply? One of the reasons I engage with you is that if you are actually sincere and have an open mind you will eventually figure out that "dismissing" things without actually refuting them is standard behavior for questions like this. And see just how hollow the dogma you have committed to is.How do you objectively divide red, orange, and yellow? I hope you don't apply this style of thinking to everything in life. See the Continuum fallacy comment above.This should be interesting. How about passing along their full reply? I think it would be interesting to try to interpret it myself.Thank you. That goes a long way towards making you seem sincere.
P.S. It would be helpful if you clarified where arguments are your own and where they have been supplied by someone else (e.g. the geneticist you consult). I get the sense there are some things being lost in translation.
He is wrong about the way he uses Fst to talk about human differences. Did you read this segment from Long et al,2009? I am not saying that Fst is useless. What I am saying is that it can not be used the way he uses it.
Apologies for not replying yet on Kevin Bird’s paper, as I said it is not my field of expertise and I need time to hear back from some people I asked on this. I am willing to consider that he might be wrong to an extent in some of his arguments as I can not judge for myself.
If you define race that way then it is not much different from the concept of population though, is it? Not subspecies as @Theodore would have it for example.
Population structure is not random, that is true. But even if a PCA overplots intermediate populations, why would you necessarily think that they are the admixed ones, instead of just giving ancestry to both populations on its extremities?
Anyways, going back at K=3. PCA shows these 3 populations distinct yes, but that does not mean large differences when actually calculating their genetic distances. Moderate differentiation at best.
Systematic sure, but multivariate methods usually show correlations no matter how weak they are.
https://pbs.twimg.com/media/D7zytYJWwAAJP4D?format=png&name=small
Sometimes I am not understanding what you are referring to. It is not vagueness on purpose. But fair enough, I will try to be more specific.
I think part of it is that I think races as formal taxonomic categories and try to use the standards used in systematics and physical anthropology to examine your argument. On the other hand, you seem to be using race as being closer to population, but correct me if I am wrong here. I can get more easily behind the 2nd concept.
I will try to give more consideration to your point of view, in any case.
The Continuum fallacy is interesting, though there are arguements against it being a fallacy. The issue with clines is that it does not allow for an objective partition of the variation which is an issue for anyone interested in human taxonomy and also makes it hard to distinguish between clusters when sampling many populations. It is why I brought it up earlier, but will not expand more on it as we are talking about k=3 here.
I can even accept that you can divide African populations in many clusters and still have races in humans, just more in Africa.
However, do not HBDers also engage in No True Scotsman? I have seen debates on the sickle cell allele, (Greeks have it for example and the response is usually something along but most Europeans dont!) or admixture ( recent East Asian admixture in Russians, Finns, Polish and many other Eastern Europeans, African admixture in southern Europeans – counter argument is but most Europeans do not! -who is most here?)
I am not saying the above examples disprove race, but just to give you an idea that it is not a fallacy used by anti-hereditarians only.
You are welcome, but my point was that expert opinion matters in those issues, why would it not?
Fair enough, but I know what I am talking about when I say he has very good arguments about why specific hereditarian claims, including human races do not exist. Alas, only by asking him you can really know so let us agree (being unable to cite specific technical statements of his here) that it is possible you are correct regarding your opinion on him.
Not sure how to pass along the actual reply but in any case, the statement was mostly along these lines:
First of all, had races existed then we would expect that the genetic distance between any two populations would be proportional to the time at which they split from a common ancestral population in the tree.
Regarding specifically the clines vs clusters issue, since clusters account for only 2% of the variation and clines for most of the variation clusters are taxonomically meaningless.
Its all in that paper that he sent me really, what I also think to be the strongest case for clines vs clusters or both clines and clustures (open to the third possibility)
https://serval.unil.ch/resource/serval:BIB_B0CA510362E4.P001/REF.pdf
An even more striking feature in the microsatellite data is that geographic distance from East Africa (the probable cradle of anatomically modern humans (e.g. Refs [19,20]) explains an impressive 85% of the smooth decrease in gene diversity (Hs) within human populations [10,12,13] (Figure 1b and Box 1 Figure Ib). Perhaps even more remarkably, similar clinal patterns can be recovered for variation in human craniometric measurements [21] and even the gut bacterium Helicobacter pylori, suggesting that this species has been commensal with human populations since our initial exit from Africa [13]. In each case, no step decrease(s) in genetic diversity were found that could be interpreted as evidence for genetic discontinuities, even at continental boundaries.
Are there papers that contradict that last sentence? Again, honestly asking, I just do not know of any.
In particular see figure 1 and their statement on the 2nd page on Native Americans and how that example can work for any clusters or continental populations.
As mentioned in the main text (Figure 1b), >75% ofthe total variance of pairwise FST can be captured by geographic distance alone. Adding information on genetic clusters to this model captures only an extra 2% of the variance
Why can then we objectively divide chimpanzees or other species? (Not all, -I know- for the same reasons as humans often)
If the paper I posted earlier does not satisfy you then I will.
As requested, I received help with the Handley et al,2007 paper I cited above. Rest are mine.
Here is a paper which looks at Wright's equation (the basis of Cochran's argument) in another context and finds it robust to violation of assumptions.
Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod
https://www.pnas.org/content/115/19/4945
Briefly, our simulations demonstrated high levels of robustness to several key assumptions, including the number of populations (two rather than infinite), their relative sizes (unequal rather than equal), and the direction of migration between them (oneway rather than two-way). We found that FST, with and without stochastic migration, rapidly approached its pseudo drift−migration equilibrium value, as expected when the number of migrants is not extremely low. These characteristics are expected to be fairly common in nature, especially for marine organisms, and facilitate the adoption of Wright’s equation in real populationsHow many times do I have to say I consider "race" and "ancestral population" essentially the same for you to get the point?Yet another false dichotomy. You do know what a false dichotomy is and understand why it is a fallacy, right? There is probably some of both, but if you think about it just a tiny bit graphically, how does admixing with intermediates maintain the extremes? It is quite obvious how admixing the extremes produces intermediates, right?You use adjectives so glibly and with so little support. Please define "Moderate differentiation" and how you determined that statement to be true.The African, East Asian, and European clusters are very clear in the PCA plots. There are intermediates to be sure (as we have discussed over and over and over), but that by no means negates the obviousness of the clusters. Which contain the majority of the population as covered in our overplotting discussion. I'm beginning to wonder exactly what points you conceded to me there since you seem to keep forgetting the points you agreed to in comment 127.You are not arguing with "HBDers" here. You are arguing with me. Stop with the red herrings (another fallacy for the collection, I feel like a bird/fallacy watcher when engaging with you). If I engage in a fallacy or reference another source which does then call me on it. What others do is irrelevant.It wasn't a compliment. Expert opinion may matter, but if what I am questioning is that very expert opinion them you see how your argument is circular, right?So he has "very good arguments" which conveniently can't be cited here. Nice. I think you know by now how much regard I have for your ability to assess argument validity.True for drift. Not necessarily true for selection. At what point will you understand that the most interesting differentiated traits are the ones which have undergone different selection pressures in different populations?Cite needed for that. You might want to ponder how much variance typically shows up in the first two PCs of PCA plots. In this paper that would be almost 11% (see Figure 1 caption):
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002886
(BTW, notice how explicit I am with my references, please try to reciprocate)At last, something concrete. Figure I (in Box 1, this is what you meant, right? Not Figure 1 on page 3) is interesting because it does not use literal geographic distance. It uses distances over estimated migration routes (which is sensible, though riddled with assumptions). You might want to make an effort to be more clear if that is the measure you intend in general.
I don't see the significance of their Native American comments. Please clarify. Be specific.
You seem to consider the lack of genetic discontinuities as some kind of kill shot. It's not. See the PCA plots. A relatively small number of intermediate people by no means invalidates the genetic distance observed between the bulk of those populations.
Distance explaining a large part of variance is completely consistent with the populations at the extremes of distance from each other (Africans, Europeans, and East Asians, once again) forming clusters.
BTW, that paper used Fst in Figure 1. Are you OK with them using it? Or is Fst only a problem when Greg Cochran uses it? You might find this worth a read: https://slatestarcodex.com/2014/08/14/beware-isolated-demands-for-rigor/Since humans and chimpanzees can't interbreed it has been possible to diverge enough (no intermediate populations remain) to make that objective. You can't objectively divide them across time though. If you follow the ancestry back to the most recent common ancestor of humans and chimpanzees there are no objective split points in between, right? Does that bother you?
On reflection, I might propose the chromosome 2 merge in humans as the split point: https://en.wikipedia.org/wiki/Chimpanzee_genome_project#Genes_of_the_chromosome_2_fusion_site
Which raises an interesting question about how we got two humans at once who were able to breed successfully. Anyone know of discussions about how changes in the number of chromosomes can actually work in that sense?I think my counterarguments demonstrate that I am not satisfied. Please do as you said.
https://twitter.com/sillyolyou/status/1224762005782958082Apologies for not replying yet on Kevin Bird's paper, as I said it is not my field of expertise and I need time to hear back from some people I asked on this. I am willing to consider that he might be wrong to an extent in some of his arguments as I can not judge for myself.If you define race that way then it is not much different from the concept of population though, is it? Not subspecies as @Theodore would have it for example.Population structure is not random, that is true. But even if a PCA overplots intermediate populations, why would you necessarily think that they are the admixed ones, instead of just giving ancestry to both populations on its extremities? Anyways, going back at K=3. PCA shows these 3 populations distinct yes, but that does not mean large differences when actually calculating their genetic distances. Moderate differentiation at best. Systematic sure, but multivariate methods usually show correlations no matter how weak they are.
https://pbs.twimg.com/media/D7zytYJWwAAJP4D?format=png&name=smallSometimes I am not understanding what you are referring to. It is not vagueness on purpose. But fair enough, I will try to be more specific.I think part of it is that I think races as formal taxonomic categories and try to use the standards used in systematics and physical anthropology to examine your argument. On the other hand, you seem to be using race as being closer to population, but correct me if I am wrong here. I can get more easily behind the 2nd concept.
I will try to give more consideration to your point of view, in any case.The Continuum fallacy is interesting, though there are arguements against it being a fallacy. The issue with clines is that it does not allow for an objective partition of the variation which is an issue for anyone interested in human taxonomy and also makes it hard to distinguish between clusters when sampling many populations. It is why I brought it up earlier, but will not expand more on it as we are talking about k=3 here. I can even accept that you can divide African populations in many clusters and still have races in humans, just more in Africa. However, do not HBDers also engage in No True Scotsman? I have seen debates on the sickle cell allele, (Greeks have it for example and the response is usually something along but most Europeans dont!) or admixture ( recent East Asian admixture in Russians, Finns, Polish and many other Eastern Europeans, African admixture in southern Europeans - counter argument is but most Europeans do not! -who is most here?)I am not saying the above examples disprove race, but just to give you an idea that it is not a fallacy used by anti-hereditarians only.You are welcome, but my point was that expert opinion matters in those issues, why would it not?Fair enough, but I know what I am talking about when I say he has very good arguments about why specific hereditarian claims, including human races do not exist. Alas, only by asking him you can really know so let us agree (being unable to cite specific technical statements of his here) that it is possible you are correct regarding your opinion on him.Not sure how to pass along the actual reply but in any case, the statement was mostly along these lines: First of all, had races existed then we would expect that the genetic distance between any two populations would be proportional to the time at which they split from a common ancestral population in the tree.
Regarding specifically the clines vs clusters issue, since clusters account for only 2% of the variation and clines for most of the variation clusters are taxonomically meaningless. Its all in that paper that he sent me really, what I also think to be the strongest case for clines vs clusters or both clines and clustures (open to the third possibility)https://serval.unil.ch/resource/serval:BIB_B0CA510362E4.P001/REF.pdf
An even more striking feature in the microsatellite data is that geographic distance from East Africa (the probable cradle of anatomically modern humans (e.g. Refs [19,20]) explains an impressive 85% of the smooth decrease in gene diversity (Hs) within human populations [10,12,13] (Figure 1b and Box 1 Figure Ib). Perhaps even more remarkably, similar clinal patterns can be recovered for variation in human craniometric measurements [21] and even the gut bacterium Helicobacter pylori, suggesting that this species has been commensal with human populations since our initial exit from Africa [13]. In each case, no step decrease(s) in genetic diversity were found that could be interpreted as evidence for genetic discontinuities, even at continental boundaries.Are there papers that contradict that last sentence? Again, honestly asking, I just do not know of any. In particular see figure 1 and their statement on the 2nd page on Native Americans and how that example can work for any clusters or continental populations. As mentioned in the main text (Figure 1b), >75% ofthe total variance of pairwise FST can be captured by geographic distance alone. Adding information on genetic clusters to this model captures only an extra 2% of the varianceWhy can then we objectively divide chimpanzees or other species? (Not all, -I know- for the same reasons as humans often)If the paper I posted earlier does not satisfy you then I will.As requested, I received help with the Handley et al,2007 paper I cited above. Rest are mine.
Before 1492, how many individual humans in history had set foot in both sub-Saharan Africa and the New World?
https://twitter.com/sillyolyou/status/1224762005782958082Apologies for not replying yet on Kevin Bird's paper, as I said it is not my field of expertise and I need time to hear back from some people I asked on this. I am willing to consider that he might be wrong to an extent in some of his arguments as I can not judge for myself.If you define race that way then it is not much different from the concept of population though, is it? Not subspecies as @Theodore would have it for example.Population structure is not random, that is true. But even if a PCA overplots intermediate populations, why would you necessarily think that they are the admixed ones, instead of just giving ancestry to both populations on its extremities? Anyways, going back at K=3. PCA shows these 3 populations distinct yes, but that does not mean large differences when actually calculating their genetic distances. Moderate differentiation at best. Systematic sure, but multivariate methods usually show correlations no matter how weak they are.
https://pbs.twimg.com/media/D7zytYJWwAAJP4D?format=png&name=smallSometimes I am not understanding what you are referring to. It is not vagueness on purpose. But fair enough, I will try to be more specific.I think part of it is that I think races as formal taxonomic categories and try to use the standards used in systematics and physical anthropology to examine your argument. On the other hand, you seem to be using race as being closer to population, but correct me if I am wrong here. I can get more easily behind the 2nd concept.
I will try to give more consideration to your point of view, in any case.The Continuum fallacy is interesting, though there are arguements against it being a fallacy. The issue with clines is that it does not allow for an objective partition of the variation which is an issue for anyone interested in human taxonomy and also makes it hard to distinguish between clusters when sampling many populations. It is why I brought it up earlier, but will not expand more on it as we are talking about k=3 here. I can even accept that you can divide African populations in many clusters and still have races in humans, just more in Africa. However, do not HBDers also engage in No True Scotsman? I have seen debates on the sickle cell allele, (Greeks have it for example and the response is usually something along but most Europeans dont!) or admixture ( recent East Asian admixture in Russians, Finns, Polish and many other Eastern Europeans, African admixture in southern Europeans - counter argument is but most Europeans do not! -who is most here?)I am not saying the above examples disprove race, but just to give you an idea that it is not a fallacy used by anti-hereditarians only.You are welcome, but my point was that expert opinion matters in those issues, why would it not?Fair enough, but I know what I am talking about when I say he has very good arguments about why specific hereditarian claims, including human races do not exist. Alas, only by asking him you can really know so let us agree (being unable to cite specific technical statements of his here) that it is possible you are correct regarding your opinion on him.Not sure how to pass along the actual reply but in any case, the statement was mostly along these lines: First of all, had races existed then we would expect that the genetic distance between any two populations would be proportional to the time at which they split from a common ancestral population in the tree.
Regarding specifically the clines vs clusters issue, since clusters account for only 2% of the variation and clines for most of the variation clusters are taxonomically meaningless. Its all in that paper that he sent me really, what I also think to be the strongest case for clines vs clusters or both clines and clustures (open to the third possibility)https://serval.unil.ch/resource/serval:BIB_B0CA510362E4.P001/REF.pdf
An even more striking feature in the microsatellite data is that geographic distance from East Africa (the probable cradle of anatomically modern humans (e.g. Refs [19,20]) explains an impressive 85% of the smooth decrease in gene diversity (Hs) within human populations [10,12,13] (Figure 1b and Box 1 Figure Ib). Perhaps even more remarkably, similar clinal patterns can be recovered for variation in human craniometric measurements [21] and even the gut bacterium Helicobacter pylori, suggesting that this species has been commensal with human populations since our initial exit from Africa [13]. In each case, no step decrease(s) in genetic diversity were found that could be interpreted as evidence for genetic discontinuities, even at continental boundaries.Are there papers that contradict that last sentence? Again, honestly asking, I just do not know of any. In particular see figure 1 and their statement on the 2nd page on Native Americans and how that example can work for any clusters or continental populations. As mentioned in the main text (Figure 1b), >75% ofthe total variance of pairwise FST can be captured by geographic distance alone. Adding information on genetic clusters to this model captures only an extra 2% of the varianceWhy can then we objectively divide chimpanzees or other species? (Not all, -I know- for the same reasons as humans often)If the paper I posted earlier does not satisfy you then I will.As requested, I received help with the Handley et al,2007 paper I cited above. Rest are mine.
Yes. Go back to the James Thompson thread and read all of the comments.
On the clines issue, in comment 63 you mention a huge hole between Greece and Turkey or something and then shown by the Oliver D Smith guy that you are wrong in comments 588 and 595.
Later in comment 625 you provide no quantitative argument against Handley's et al,2007 analysis and in comment 632 you just hand-wave Templeton's analysis away.
At some point you mention something about looking into Fst values but you never posted any.
In comment 659 you even state yourself that you do not understand the figure (correlation of genetic distance with geographic distance).
In comment 714, Oliver D Smith mentions that Fst values under 1% approach panmixia, again no quantitative reply. No reply to comments 736 and 737 either and an ad hom from you in comment 739.
So how exactly did anything in the Thompson thread proves me wrong?
None most likely (possible but unlikely exception a Viking in the 9th century) but why is this relevant?
Is not most of this discussion about Europeans and Africans and East Asians?
I will look and get back to you.
These are the standards people use not only in anthropology but genetics. I have had conversations with geneticists, been to some seminars and read a fair amount of papers. I am not making them up.I study human evolution and like many others who do (from various fields) I am interested in evolutionary relationships of populations. A race that is defined by shared phenotype like Africans tells me little about their evolutionary history (beyond skin color or perhaps other phenotypic traits) if they do not share a genetic connection stronger than that with other populations or races as you would call them. Something that helps us understand their demographic history, detect selection etc.
I do not know if it is feasible for you or not, but that blog with the cophenetic relationship seems interesting. If his result can be replicated (I do not have the software to do so) then that is a good measure of races (even if it is k=3 like we said, means these groups have evolved in enough isolation and are sufficiently different even excluding intermediate populations)Kevin also used the Lee et al data to prove his argument.
But, let me read more about this and will get back to you. It is not my field of expertise.
I know. I think I have made clear I was aware of those arguments before I ever encountered you. I just don’t find them convincing. And you treat them as gospel. I believe I have provided cogent responses countering those arguments. Which you have responded to mostly by just repeating them.
I am baffled how you can assert the things you describe are not true. The PCA plots make the strength of the genetic clustering very clear. I thought you had agreed this was the case for Africans, East Asians, and Europeans.
I think Pumpkin Person’s observation is straightforward, but his procedure uses group averages so obscures the within group variation. I think we really need to do it with a full dataset of individuals, which is more work than I want to take on. Link back to PP’s post:
https://pumpkinperson.com/2019/05/28/genetic-distance-the-cophenetic-correlation/
Yes. Bird seems to agree that the Lee et al. data and analysis are good. Which supports my original point. From comment 110: “How can you say “they have not been found and are unlikely to” given the progress we have seen in GWAS for these traits?”
So your argument quoted above is an affirmation of my point, not a rebuttal. Care to try again one more time? Or perhaps it would be better for you to stop digging this particular hole deeper?
Usually these PCAs only use YRI for example which represents West Africans and to an extent Bantu Speakers. I was linked to this paper, I would be interested in your thoughts on their PCA.
https://www.researchgate.net/figure/fig2_24394165It is, I would just be curious to see if it would replicate. To my knowledge, he is the only one besides Templeton who tried this for humans and his tree seems robust which if confirmed by any other analyses I think would give credence to your position on race. It is this part that makes me think he might have done something wrong as he states so himselfCurrent PGS including Lee et al are not casual, are they? And Kevin's analysis demonstrates how unlikely these variants are to differ between populations.
https://twitter.com/sillyolyou/status/1224762005782958082Apologies for not replying yet on Kevin Bird's paper, as I said it is not my field of expertise and I need time to hear back from some people I asked on this. I am willing to consider that he might be wrong to an extent in some of his arguments as I can not judge for myself.If you define race that way then it is not much different from the concept of population though, is it? Not subspecies as @Theodore would have it for example.Population structure is not random, that is true. But even if a PCA overplots intermediate populations, why would you necessarily think that they are the admixed ones, instead of just giving ancestry to both populations on its extremities? Anyways, going back at K=3. PCA shows these 3 populations distinct yes, but that does not mean large differences when actually calculating their genetic distances. Moderate differentiation at best. Systematic sure, but multivariate methods usually show correlations no matter how weak they are.
https://pbs.twimg.com/media/D7zytYJWwAAJP4D?format=png&name=smallSometimes I am not understanding what you are referring to. It is not vagueness on purpose. But fair enough, I will try to be more specific.I think part of it is that I think races as formal taxonomic categories and try to use the standards used in systematics and physical anthropology to examine your argument. On the other hand, you seem to be using race as being closer to population, but correct me if I am wrong here. I can get more easily behind the 2nd concept.
I will try to give more consideration to your point of view, in any case.The Continuum fallacy is interesting, though there are arguements against it being a fallacy. The issue with clines is that it does not allow for an objective partition of the variation which is an issue for anyone interested in human taxonomy and also makes it hard to distinguish between clusters when sampling many populations. It is why I brought it up earlier, but will not expand more on it as we are talking about k=3 here. I can even accept that you can divide African populations in many clusters and still have races in humans, just more in Africa. However, do not HBDers also engage in No True Scotsman? I have seen debates on the sickle cell allele, (Greeks have it for example and the response is usually something along but most Europeans dont!) or admixture ( recent East Asian admixture in Russians, Finns, Polish and many other Eastern Europeans, African admixture in southern Europeans - counter argument is but most Europeans do not! -who is most here?)I am not saying the above examples disprove race, but just to give you an idea that it is not a fallacy used by anti-hereditarians only.You are welcome, but my point was that expert opinion matters in those issues, why would it not?Fair enough, but I know what I am talking about when I say he has very good arguments about why specific hereditarian claims, including human races do not exist. Alas, only by asking him you can really know so let us agree (being unable to cite specific technical statements of his here) that it is possible you are correct regarding your opinion on him.Not sure how to pass along the actual reply but in any case, the statement was mostly along these lines: First of all, had races existed then we would expect that the genetic distance between any two populations would be proportional to the time at which they split from a common ancestral population in the tree.
Regarding specifically the clines vs clusters issue, since clusters account for only 2% of the variation and clines for most of the variation clusters are taxonomically meaningless. Its all in that paper that he sent me really, what I also think to be the strongest case for clines vs clusters or both clines and clustures (open to the third possibility)https://serval.unil.ch/resource/serval:BIB_B0CA510362E4.P001/REF.pdf
An even more striking feature in the microsatellite data is that geographic distance from East Africa (the probable cradle of anatomically modern humans (e.g. Refs [19,20]) explains an impressive 85% of the smooth decrease in gene diversity (Hs) within human populations [10,12,13] (Figure 1b and Box 1 Figure Ib). Perhaps even more remarkably, similar clinal patterns can be recovered for variation in human craniometric measurements [21] and even the gut bacterium Helicobacter pylori, suggesting that this species has been commensal with human populations since our initial exit from Africa [13]. In each case, no step decrease(s) in genetic diversity were found that could be interpreted as evidence for genetic discontinuities, even at continental boundaries.Are there papers that contradict that last sentence? Again, honestly asking, I just do not know of any. In particular see figure 1 and their statement on the 2nd page on Native Americans and how that example can work for any clusters or continental populations. As mentioned in the main text (Figure 1b), >75% ofthe total variance of pairwise FST can be captured by geographic distance alone. Adding information on genetic clusters to this model captures only an extra 2% of the varianceWhy can then we objectively divide chimpanzees or other species? (Not all, -I know- for the same reasons as humans often)If the paper I posted earlier does not satisfy you then I will.As requested, I received help with the Handley et al,2007 paper I cited above. Rest are mine.
Yet another false dichotomy. The question is how serious the violation of assumptions is and how much it invalidates his point. His post again: https://westhunt.wordpress.com/2019/01/07/gene-flow/
Here is a paper which looks at Wright’s equation (the basis of Cochran’s argument) in another context and finds it robust to violation of assumptions.
Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod
https://www.pnas.org/content/115/19/4945
Briefly, our simulations demonstrated high levels of robustness to several key assumptions, including the number of populations (two rather than infinite), their relative sizes (unequal rather than equal), and the direction of migration between them (oneway rather than two-way). We found that FST, with and without stochastic migration, rapidly approached its pseudo drift−migration equilibrium value, as expected when the number of migrants is not extremely low. These characteristics are expected to be fairly common in nature, especially for marine organisms, and facilitate the adoption of Wright’s equation in real populations
How many times do I have to say I consider “race” and “ancestral population” essentially the same for you to get the point?
Yet another false dichotomy. You do know what a false dichotomy is and understand why it is a fallacy, right? There is probably some of both, but if you think about it just a tiny bit graphically, how does admixing with intermediates maintain the extremes? It is quite obvious how admixing the extremes produces intermediates, right?
You use adjectives so glibly and with so little support. Please define “Moderate differentiation” and how you determined that statement to be true.
The African, East Asian, and European clusters are very clear in the PCA plots. There are intermediates to be sure (as we have discussed over and over and over), but that by no means negates the obviousness of the clusters. Which contain the majority of the population as covered in our overplotting discussion. I’m beginning to wonder exactly what points you conceded to me there since you seem to keep forgetting the points you agreed to in comment 127.
You are not arguing with “HBDers” here. You are arguing with me. Stop with the red herrings (another fallacy for the collection, I feel like a bird/fallacy watcher when engaging with you). If I engage in a fallacy or reference another source which does then call me on it. What others do is irrelevant.
It wasn’t a compliment. Expert opinion may matter, but if what I am questioning is that very expert opinion them you see how your argument is circular, right?
So he has “very good arguments” which conveniently can’t be cited here. Nice. I think you know by now how much regard I have for your ability to assess argument validity.
True for drift. Not necessarily true for selection. At what point will you understand that the most interesting differentiated traits are the ones which have undergone different selection pressures in different populations?
Cite needed for that. You might want to ponder how much variance typically shows up in the first two PCs of PCA plots. In this paper that would be almost 11% (see Figure 1 caption):
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002886
(BTW, notice how explicit I am with my references, please try to reciprocate)
At last, something concrete. Figure I (in Box 1, this is what you meant, right? Not Figure 1 on page 3) is interesting because it does not use literal geographic distance. It uses distances over estimated migration routes (which is sensible, though riddled with assumptions). You might want to make an effort to be more clear if that is the measure you intend in general.
I don’t see the significance of their Native American comments. Please clarify. Be specific.
You seem to consider the lack of genetic discontinuities as some kind of kill shot. It’s not. See the PCA plots. A relatively small number of intermediate people by no means invalidates the genetic distance observed between the bulk of those populations.
Distance explaining a large part of variance is completely consistent with the populations at the extremes of distance from each other (Africans, Europeans, and East Asians, once again) forming clusters.
BTW, that paper used Fst in Figure 1. Are you OK with them using it? Or is Fst only a problem when Greg Cochran uses it? You might find this worth a read: https://slatestarcodex.com/2014/08/14/beware-isolated-demands-for-rigor/
Since humans and chimpanzees can’t interbreed it has been possible to diverge enough (no intermediate populations remain) to make that objective. You can’t objectively divide them across time though. If you follow the ancestry back to the most recent common ancestor of humans and chimpanzees there are no objective split points in between, right? Does that bother you?
On reflection, I might propose the chromosome 2 merge in humans as the split point: https://en.wikipedia.org/wiki/Chimpanzee_genome_project#Genes_of_the_chromosome_2_fusion_site
Which raises an interesting question about how we got two humans at once who were able to breed successfully. Anyone know of discussions about how changes in the number of chromosomes can actually work in that sense?
I think my counterarguments demonstrate that I am not satisfied. Please do as you said.
https://www.sciencemag.org/news/2014/08/geneticists-decry-book-race-and-evolution
My point was that it is clear where he stands on this debate, as for technical arguments, I can cite how he disagrees with clusters such as those in the Rosenberg study race realists often cite, how we all share recent ancestry or how isolation-by-distance better explains patterns of genetic diversity in humans.No, I understand that, but most of the genome is neutral. Selection has not acted on that many traits (see Coop's 2009 for this). Skin and hair pigmentation etc, some medical variants but not a lot of evidence for differential selection between ancestral populations in IQ for example. Or at least, has not been detected thus far.Sure, the significance is that even where there seem to be splits between populations, the process is much more complex than often assumed. There has been some gene flow between North America and Asia too, even after colonization some 15.000 years back.No, because differentiation has already happened. I told you, had phylogenomic methods proved lineages for humans just as they do between humans and chimpanzees (let's say that a paper comes out tomorrow that suggests that demographic inferences have been biased so far or something) then I would have no issue acknowledging races in humans.not the best example maybe, but yes, chromosome changes can facilitate reproductive isolation. Will have to look more into this specific case: https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14874
(I am not citing anything from the paper just to keep this short- I think it helps make your point though but I might be wrong)To keep this concise, I will expand on your points based on the geneticist's reply and cited papers:
https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12816
By reviewing the literature on structure performance in IBD data sets, we found a high number of studies showing that structure outputs are extremely affected by IBD. This misleading inference results principally in the detection of artificial genetic clusters. The literature survey showed that IBD was present in most data sets (60.56%) and that a substantial number of the articles only tested IBD by Mantel tests (82.21%). The most concerning result is that several articles have been using structure even after detecting IBD (57.99%), and a substantial number of them are drawing formal conservation strategies, notwithstanding the potentially biased results (51.49%).
Results obtained indicate that sampling from pre‐defined populations affects more the results of analyses than sampling individuals evenly distributed across the landscape (Aurelle & Ledoux, 2013; Kalinowski, 2011; Rosenberg et al., 2005; Schwartz & McKelvey, 2009).
However, this software showed biased performance by detecting artificial clusters in data sets containing clines of genetic variation (Frantz et al., 2009; Guillot et al., 2009; Rosenberg et al., 2005), a pattern expected as a result of IBD. The software's authors recognized this shortfall, and since 2002, the following sentence regarding IBD is stated in the structure manual (Pritchard & Wen, 2002): “In this situation, allele frequencies vary gradually across the region. The underlying structure model is not well suited to data from this kind of scenario. When this occurs, the inferred value of K, and the corresponding allele frequencies in each group can be rather arbitrary.”
Since STRUCTURE clusters are affected by sampling, we would expect PCA plots to be as well due to IBD.
The limitations of PCA for investigating population structure in a spatio-temporal context highlights the need for new theoretical developments to analyze population structure when present-day and ancient samples are combined. This is especially apparent when considering the complex demographic scenarios already inferred about the history of modern humans (Pickrell and Reich,
2014). Important theoretical work has already been done to test specific hypothesis (Durand et al., 2011; Loh et al., 2013). Another way to test different past demographic events is with simulationintensive methods, such as Approximate Bayesian Computations (Beaumont et al., 2002; Csilléry et al., 2010). In this case, theoretical developments on mechanistic models such as the stepping-stone model are important to perform simulations efficiently (Baird and
Santos, 2010).
If I am not wrong, the above papers means that humans follow an entirely clinal pattern of genetic variance, and even the clusters identified in the Rosenberg study are an artifact of IBD.
I will cite Kevin here, as he explains the 2nd point pretty well:
https://twitter.com/itsbirdemic/status/1226212010255409154
Further analyses revealed even stronger geographic patterns or ‘clines’ (see Glossary): genetic distance between populations increased with geographic distance at both continental and global scales [5,6], which is characteristic of so-called ‘isolation by distance’ (IBD) [7] models.
So it seems to be almost (if not) entirely a clinal world, without any real clusters.
More after your reply, I was linked to 2 additional papers but want to keep it short. And yes these papers were linked to me from the geneticist.
https://pumpkinperson.com/2019/05/28/genetic-distance-the-cophenetic-correlation/Yes. Bird seems to agree that the Lee et al. data and analysis are good. Which supports my original point. From comment 110: "How can you say “they have not been found and are unlikely to” given the progress we have seen in GWAS for these traits?"
So your argument quoted above is an affirmation of my point, not a rebuttal. Care to try again one more time? Or perhaps it would be better for you to stop digging this particular hole deeper?
Sure, I was speaking about within Africa variation. That Africans, East Asians and Europeans are distinct on a PCA does not negate differences within those groups. In particular Africans.
Africans can all be distinct from Europeans but that does not mean they are not distinct from each other when sampled over the entire continent.
Usually these PCAs only use YRI for example which represents West Africans and to an extent Bantu Speakers.
I was linked to this paper, I would be interested in your thoughts on their PCA.
https://www.researchgate.net/figure/fig2_24394165
It is, I would just be curious to see if it would replicate. To my knowledge, he is the only one besides Templeton who tried this for humans and his tree seems robust which if confirmed by any other analyses I think would give credence to your position on race.
It is this part that makes me think he might have done something wrong as he states so himself
Current PGS including Lee et al are not casual, are they? And Kevin’s analysis demonstrates how unlikely these variants are to differ between populations.
From the paper the percent variance explained for the first three global PCs is 19.5%, 5.01%, and 3.5%. That makes clear how much the non/African split dominates things. Within Africa the percent variance explained for the first three PCs is 10.8%, 6.1%, and 4.9%. Actually, their full explanations of these are interesting, so:Back to you.Lee actually looks at this some (you have read the paper, right? if not go do that and stop wasting my time). A sample: "relative to other genes, genes near our lead SNPs are overwhelmingly enriched for expression in the central nervous system"
Other GWAS make more of an attempt to look at causality. Like the one I linked just above in comment 126 (referencing tissue types). Why do you keep raising issues I have already addressed?Then his analysis is wrong somehow, because we see that those variants do differ between populations in reality. Piffer's work using Lee's EDU PGS shows that quite clearly. You can argue about whether it is OK to use the PGS between populations to show phenotypes, but I don't think it is arguable that Piffer's PGS results show the frequency variation. Would you be more convinced if we looked at the distribution of particular variants? That is easy to do with GGV
https://popgen.uchicago.edu/ggv/?data=%221000genomes%22&chr=1&pos=222087833
You might take a look at rs61734410 mentioned in Lee's paper and compare the frequencies in East Asia to elsewhere.
I list some more SNPs in this comment:
https://www.unz.com/jthompson/the-worlds-iq-86/?showcomments#comment-2071349
Or you can do the heavy lifting yourself and go look at Lee's list.
So I did look and I do not see how anything said (by you at least) supports your position:
On the clines issue, in comment 63 you mention a huge hole between Greece and Turkey or something and then shown by the Oliver D Smith guy that you are wrong in comments 588 and 595.
Later in comment 625 you provide no quantitative argument against Handley’s et al,2007 analysis and in comment 632 you just hand-wave Templeton’s analysis away.
At some point you mention something about looking into Fst values but you never posted any.
In comment 659 you even state yourself that you do not understand the figure (correlation of genetic distance with geographic distance).
In comment 714, Oliver D Smith mentions that Fst values under 1% approach panmixia, again no quantitative reply. No reply to comments 736 and 737 either and an ad hom from you in comment 739.
So how exactly did anything in the Thompson thread proves me wrong?
Usually these PCAs only use YRI for example which represents West Africans and to an extent Bantu Speakers. I was linked to this paper, I would be interested in your thoughts on their PCA.
https://www.researchgate.net/figure/fig2_24394165It is, I would just be curious to see if it would replicate. To my knowledge, he is the only one besides Templeton who tried this for humans and his tree seems robust which if confirmed by any other analyses I think would give credence to your position on race. It is this part that makes me think he might have done something wrong as he states so himselfCurrent PGS including Lee et al are not casual, are they? And Kevin's analysis demonstrates how unlikely these variants are to differ between populations.
No kidding. There is a reason I keep saying race is hierarchical.
I am soon going to stop responding to comments like this unless you start offering your opinion first. I am exceedingly tired of this “what do you think” game.
From the paper the percent variance explained for the first three global PCs is 19.5%, 5.01%, and 3.5%. That makes clear how much the non/African split dominates things. Within Africa the percent variance explained for the first three PCs is 10.8%, 6.1%, and 4.9%. Actually, their full explanations of these are interesting, so:
Back to you.
Lee actually looks at this some (you have read the paper, right? if not go do that and stop wasting my time). A sample: “relative to other genes, genes near our lead SNPs are overwhelmingly enriched for expression in the central nervous system”
Other GWAS make more of an attempt to look at causality. Like the one I linked just above in comment 126 (referencing tissue types). Why do you keep raising issues I have already addressed?
Then his analysis is wrong somehow, because we see that those variants do differ between populations in reality. Piffer’s work using Lee’s EDU PGS shows that quite clearly. You can argue about whether it is OK to use the PGS between populations to show phenotypes, but I don’t think it is arguable that Piffer’s PGS results show the frequency variation. Would you be more convinced if we looked at the distribution of particular variants? That is easy to do with GGV
https://popgen.uchicago.edu/ggv/?data=%221000genomes%22&chr=1&pos=222087833
You might take a look at rs61734410 mentioned in Lee’s paper and compare the frequencies in East Asia to elsewhere.
I list some more SNPs in this comment:
https://www.unz.com/jthompson/the-worlds-iq-86/?showcomments#comment-2071349
Or you can do the heavy lifting yourself and go look at Lee’s list.
First, regarding the clusters from the HGDP etc studies, here is an article from my own field:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941216/pdf/cshperspect-DIV-a021238.pdf
How these criteria reflect real history as well as the analysis itself may vary with the software
program used in the admixture analysis, and each program has its own assumptions and
methods, which can affect the results. For example, the investigators of the original modern
admixture program called STRUCTURE (Pritchard et al. 2000) clearly provide all of the appropriate caveats, in clear terms, and most importantly the subjective judgments required in interpretation and that the program is designed to estimate admixture history even when admixture is an appropriate way to view what actually happened (if that is even known).
However, most nonshared variants will only be found in some individuals in a purported race’s geographic homeland. That might seem to imply rather strangely that, depending on how definitions are operationalized, members of a purported race would not have all
of its defining alleles! This shows how what one chooses to sample can affect or even predetermine the results. That is not supposed to happen in science.
It is too long to cite here, but do take a look at their simulations in pages 10-12 as they show how artificial clusters are.
More on PCAs: https://www.genetics.org/content/211/1/289.abstract that also shows how assumptions on Fst can distort detection of selection etc that studies like Lee et al use:
"It is common to describe variation along the genome of simple statistics such as FST and to interpret the results in terms of the action of selection (e.g., Turner et al. 2005;
Ellegren et al. 2012). However, a given pattern (e.g., valleys of FST) can be caused by more than one biological process (Cruickshank and Hahn 2014; Burri et al. 2015), which in retrospect is unsurprising given that we are using a single statistic to describe a complex process. It is also common to use methods such as PCA to visualize large-scale patterns in mean genome-wide relatedness. In this paper, we show if and how patterns of mean relatedness vary systematically along the genome, in a way particularly suited to large samples from geographically distributed populations. Geographic population structure sets the stage by establishing background patterns of relatedness, our method then describes how this structure is affected by selection and other factors.
The method is descriptive: it does not aim to identify outlier loci, but rather to describe larger-scale variation shared by many parts of the genome and give clues about the source of
this variation."
On the clines issue, in comment 63 you mention a huge hole between Greece and Turkey or something and then shown by the Oliver D Smith guy that you are wrong in comments 588 and 595.
Later in comment 625 you provide no quantitative argument against Handley's et al,2007 analysis and in comment 632 you just hand-wave Templeton's analysis away.
At some point you mention something about looking into Fst values but you never posted any.
In comment 659 you even state yourself that you do not understand the figure (correlation of genetic distance with geographic distance).
In comment 714, Oliver D Smith mentions that Fst values under 1% approach panmixia, again no quantitative reply. No reply to comments 736 and 737 either and an ad hom from you in comment 739.
So how exactly did anything in the Thompson thread proves me wrong?
Naturally you are going to claim that you were correct and nobody could prove you wrong. Anyone who is interested can go and check that.
Here is a paper which looks at Wright's equation (the basis of Cochran's argument) in another context and finds it robust to violation of assumptions.
Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod
https://www.pnas.org/content/115/19/4945
Briefly, our simulations demonstrated high levels of robustness to several key assumptions, including the number of populations (two rather than infinite), their relative sizes (unequal rather than equal), and the direction of migration between them (oneway rather than two-way). We found that FST, with and without stochastic migration, rapidly approached its pseudo drift−migration equilibrium value, as expected when the number of migrants is not extremely low. These characteristics are expected to be fairly common in nature, especially for marine organisms, and facilitate the adoption of Wright’s equation in real populationsHow many times do I have to say I consider "race" and "ancestral population" essentially the same for you to get the point?Yet another false dichotomy. You do know what a false dichotomy is and understand why it is a fallacy, right? There is probably some of both, but if you think about it just a tiny bit graphically, how does admixing with intermediates maintain the extremes? It is quite obvious how admixing the extremes produces intermediates, right?You use adjectives so glibly and with so little support. Please define "Moderate differentiation" and how you determined that statement to be true.The African, East Asian, and European clusters are very clear in the PCA plots. There are intermediates to be sure (as we have discussed over and over and over), but that by no means negates the obviousness of the clusters. Which contain the majority of the population as covered in our overplotting discussion. I'm beginning to wonder exactly what points you conceded to me there since you seem to keep forgetting the points you agreed to in comment 127.You are not arguing with "HBDers" here. You are arguing with me. Stop with the red herrings (another fallacy for the collection, I feel like a bird/fallacy watcher when engaging with you). If I engage in a fallacy or reference another source which does then call me on it. What others do is irrelevant.It wasn't a compliment. Expert opinion may matter, but if what I am questioning is that very expert opinion them you see how your argument is circular, right?So he has "very good arguments" which conveniently can't be cited here. Nice. I think you know by now how much regard I have for your ability to assess argument validity.True for drift. Not necessarily true for selection. At what point will you understand that the most interesting differentiated traits are the ones which have undergone different selection pressures in different populations?Cite needed for that. You might want to ponder how much variance typically shows up in the first two PCs of PCA plots. In this paper that would be almost 11% (see Figure 1 caption):
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002886
(BTW, notice how explicit I am with my references, please try to reciprocate)At last, something concrete. Figure I (in Box 1, this is what you meant, right? Not Figure 1 on page 3) is interesting because it does not use literal geographic distance. It uses distances over estimated migration routes (which is sensible, though riddled with assumptions). You might want to make an effort to be more clear if that is the measure you intend in general.
I don't see the significance of their Native American comments. Please clarify. Be specific.
You seem to consider the lack of genetic discontinuities as some kind of kill shot. It's not. See the PCA plots. A relatively small number of intermediate people by no means invalidates the genetic distance observed between the bulk of those populations.
Distance explaining a large part of variance is completely consistent with the populations at the extremes of distance from each other (Africans, Europeans, and East Asians, once again) forming clusters.
BTW, that paper used Fst in Figure 1. Are you OK with them using it? Or is Fst only a problem when Greg Cochran uses it? You might find this worth a read: https://slatestarcodex.com/2014/08/14/beware-isolated-demands-for-rigor/Since humans and chimpanzees can't interbreed it has been possible to diverge enough (no intermediate populations remain) to make that objective. You can't objectively divide them across time though. If you follow the ancestry back to the most recent common ancestor of humans and chimpanzees there are no objective split points in between, right? Does that bother you?
On reflection, I might propose the chromosome 2 merge in humans as the split point: https://en.wikipedia.org/wiki/Chimpanzee_genome_project#Genes_of_the_chromosome_2_fusion_site
Which raises an interesting question about how we got two humans at once who were able to breed successfully. Anyone know of discussions about how changes in the number of chromosomes can actually work in that sense?I think my counterarguments demonstrate that I am not satisfied. Please do as you said.
Fair enough, that is a definition that I think is more reasonable.
But we know from ancient DNA that modern-day Near Easterners gave ancestry to Europeans during the Neolithic.
He is extremely skeptical of HBD papers and books, even starting the letter against Nicholas Wade when he represented population genetics research.
https://www.sciencemag.org/news/2014/08/geneticists-decry-book-race-and-evolution
My point was that it is clear where he stands on this debate, as for technical arguments, I can cite how he disagrees with clusters such as those in the Rosenberg study race realists often cite, how we all share recent ancestry or how isolation-by-distance better explains patterns of genetic diversity in humans.
No, I understand that, but most of the genome is neutral. Selection has not acted on that many traits (see Coop’s 2009 for this). Skin and hair pigmentation etc, some medical variants but not a lot of evidence for differential selection between ancestral populations in IQ for example. Or at least, has not been detected thus far.
Sure, the significance is that even where there seem to be splits between populations, the process is much more complex than often assumed. There has been some gene flow between North America and Asia too, even after colonization some 15.000 years back.
No, because differentiation has already happened. I told you, had phylogenomic methods proved lineages for humans just as they do between humans and chimpanzees (let’s say that a paper comes out tomorrow that suggests that demographic inferences have been biased so far or something) then I would have no issue acknowledging races in humans.
not the best example maybe, but yes, chromosome changes can facilitate reproductive isolation. Will have to look more into this specific case: https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14874
(I am not citing anything from the paper just to keep this short- I think it helps make your point though but I might be wrong)
To keep this concise, I will expand on your points based on the geneticist’s reply and cited papers:
https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12816
By reviewing the literature on structure performance in IBD data sets, we found a high number of studies showing that structure outputs are extremely affected by IBD. This misleading inference results principally in the detection of artificial genetic clusters. The literature survey showed that IBD was present in most data sets (60.56%) and that a substantial number of the articles only tested IBD by Mantel tests (82.21%). The most concerning result is that several articles have been using structure even after detecting IBD (57.99%), and a substantial number of them are drawing formal conservation strategies, notwithstanding the potentially biased results (51.49%).
Results obtained indicate that sampling from pre‐defined populations affects more the results of analyses than sampling individuals evenly distributed across the landscape (Aurelle & Ledoux, 2013; Kalinowski, 2011; Rosenberg et al., 2005; Schwartz & McKelvey, 2009).
However, this software showed biased performance by detecting artificial clusters in data sets containing clines of genetic variation (Frantz et al., 2009; Guillot et al., 2009; Rosenberg et al., 2005), a pattern expected as a result of IBD. The software’s authors recognized this shortfall, and since 2002, the following sentence regarding IBD is stated in the structure manual (Pritchard & Wen, 2002): “In this situation, allele frequencies vary gradually across the region. The underlying structure model is not well suited to data from this kind of scenario. When this occurs, the inferred value of K, and the corresponding allele frequencies in each group can be rather arbitrary.”
Since STRUCTURE clusters are affected by sampling, we would expect PCA plots to be as well due to IBD.
The limitations of PCA for investigating population structure in a spatio-temporal context highlights the need for new theoretical developments to analyze population structure when present-day and ancient samples are combined. This is especially apparent when considering the complex demographic scenarios already inferred about the history of modern humans (Pickrell and Reich,
2014). Important theoretical work has already been done to test specific hypothesis (Durand et al., 2011; Loh et al., 2013). Another way to test different past demographic events is with simulationintensive methods, such as Approximate Bayesian Computations (Beaumont et al., 2002; Csilléry et al., 2010). In this case, theoretical developments on mechanistic models such as the stepping-stone model are important to perform simulations efficiently (Baird and
Santos, 2010).
If I am not wrong, the above papers means that humans follow an entirely clinal pattern of genetic variance, and even the clusters identified in the Rosenberg study are an artifact of IBD.
I will cite Kevin here, as he explains the 2nd point pretty well:
Further analyses revealed even stronger geographic patterns or ‘clines’ (see Glossary): genetic distance between populations increased with geographic distance at both continental and global scales [5,6], which is characteristic of so-called ‘isolation by distance’ (IBD) [7] models.
So it seems to be almost (if not) entirely a clinal world, without any real clusters.
More after your reply, I was linked to 2 additional papers but want to keep it short. And yes these papers were linked to me from the geneticist.
Remember that population genetics is under tension from isolation producing differences and mixing muting those differences. And this is all happening concurrent with selection.You say that like it is a feature. To my mind all you said there is how biased he is.How about more citing and less talking about how you could do so? To preempt some of the less useful conversations.
- No need to talk about the false dichotomy of IBD vs. other explanations. As I discuss below, what is important is that the differences exist.
- Sharing recent ancestry is pretty much given. What matters is the scope of the remaining differences.
- When "disagreeing with" clusters (what does that even mean?) focus on the actual data, not the causes.
If you do care to introduce specific arguments of his, how about doing so in individual comments? This would make it easier to track the progress of each individual argument.Please include links.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000500
This is one of the more interesting papers you have referenced.
One thing I think Coop has neglected to consider adequately is the possibility (prevalence) of balancing selection ("balanc" appears in his paper only in the title of one of his references).
https://en.wikipedia.org/wiki/Balancing_selection
That is a strange omission for as expert a geneticist as he is. Consider the sickle cell allele. The frequency differences never become that large because the homozygous recessive case causes disease.
I suppose that is partly covered (implicitly) in this excerpt. I think this makes clear the abstract oversimplifies things in a way your argument depends on.
We propose below that even if positive selection is common in the genome, strong selection that drives new mutations rapidly to fixation appears to be rare. Our results also argue against a strong form of adaptation in local populations by very large allele frequency shifts at individual loci. However, our data do not preclude a weaker level of adaptive tuning: i.e., modest frequency changes may often occur in response to local conditions [23],[24],[52]. Indeed, it is still possible that small frequency shifts at multiple loci could allow populations to effectively adapt to local conditions even in the absence of large frequency changes at individual loci.
Contrast that to your summary of Coop: "Selection has not acted on that many traits"
I think it is clear he is not asserting that. I am trying to decide whether your misleading summaries are due to ignorance (not reading and understanding the papers) or agenda (of course, both is always an option, I can think past false dichotomies). BTW, when you do things like that and then just move on to another (usually bad as well) argument when called on it, that's a Gish gallop.
Regarding evidence for IQ selection, two points:
- Do you sincerely think IQ has not been selected for? If not then it is clear it is just a matter of finding the evidence.
- I think the presence of significantly differentiated SNPs (discussed elsewhere) serves as evidence.Do you have any idea how tedious your vague "appeals to complexity" are? If you think I have been overly simplistic about something then call it out. Otherwise just be quiet about what is "often assumed." It is not germane to our conversation.So you don't care that you can't put a finger on where differentiation actually happened. Rather inconsistent with your demands for objective splits in the present. I'm not even sure what the rest of that paragraph means. But I am pretty sure it's not worth the effort to understand.How many times do I have to say I consider IBD a cause of race? Why the differences are present matters much less than that they ARE present.So you are retracting your earlier agreement with my statement?At this point you are looking like an insincere intellectual lightweight who is serving as a mouthpiece for someone who is only slightly better informed and afraid to come here and debate for himself.
Yeah, okay when you decide to reply with an argument to the points raised about clines and clusters for example, let me know.
https://www.sciencemag.org/news/2014/08/geneticists-decry-book-race-and-evolution
My point was that it is clear where he stands on this debate, as for technical arguments, I can cite how he disagrees with clusters such as those in the Rosenberg study race realists often cite, how we all share recent ancestry or how isolation-by-distance better explains patterns of genetic diversity in humans.No, I understand that, but most of the genome is neutral. Selection has not acted on that many traits (see Coop's 2009 for this). Skin and hair pigmentation etc, some medical variants but not a lot of evidence for differential selection between ancestral populations in IQ for example. Or at least, has not been detected thus far.Sure, the significance is that even where there seem to be splits between populations, the process is much more complex than often assumed. There has been some gene flow between North America and Asia too, even after colonization some 15.000 years back.No, because differentiation has already happened. I told you, had phylogenomic methods proved lineages for humans just as they do between humans and chimpanzees (let's say that a paper comes out tomorrow that suggests that demographic inferences have been biased so far or something) then I would have no issue acknowledging races in humans.not the best example maybe, but yes, chromosome changes can facilitate reproductive isolation. Will have to look more into this specific case: https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14874
(I am not citing anything from the paper just to keep this short- I think it helps make your point though but I might be wrong)To keep this concise, I will expand on your points based on the geneticist's reply and cited papers:
https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12816
By reviewing the literature on structure performance in IBD data sets, we found a high number of studies showing that structure outputs are extremely affected by IBD. This misleading inference results principally in the detection of artificial genetic clusters. The literature survey showed that IBD was present in most data sets (60.56%) and that a substantial number of the articles only tested IBD by Mantel tests (82.21%). The most concerning result is that several articles have been using structure even after detecting IBD (57.99%), and a substantial number of them are drawing formal conservation strategies, notwithstanding the potentially biased results (51.49%).
Results obtained indicate that sampling from pre‐defined populations affects more the results of analyses than sampling individuals evenly distributed across the landscape (Aurelle & Ledoux, 2013; Kalinowski, 2011; Rosenberg et al., 2005; Schwartz & McKelvey, 2009).
However, this software showed biased performance by detecting artificial clusters in data sets containing clines of genetic variation (Frantz et al., 2009; Guillot et al., 2009; Rosenberg et al., 2005), a pattern expected as a result of IBD. The software's authors recognized this shortfall, and since 2002, the following sentence regarding IBD is stated in the structure manual (Pritchard & Wen, 2002): “In this situation, allele frequencies vary gradually across the region. The underlying structure model is not well suited to data from this kind of scenario. When this occurs, the inferred value of K, and the corresponding allele frequencies in each group can be rather arbitrary.”
Since STRUCTURE clusters are affected by sampling, we would expect PCA plots to be as well due to IBD.
The limitations of PCA for investigating population structure in a spatio-temporal context highlights the need for new theoretical developments to analyze population structure when present-day and ancient samples are combined. This is especially apparent when considering the complex demographic scenarios already inferred about the history of modern humans (Pickrell and Reich,
2014). Important theoretical work has already been done to test specific hypothesis (Durand et al., 2011; Loh et al., 2013). Another way to test different past demographic events is with simulationintensive methods, such as Approximate Bayesian Computations (Beaumont et al., 2002; Csilléry et al., 2010). In this case, theoretical developments on mechanistic models such as the stepping-stone model are important to perform simulations efficiently (Baird and
Santos, 2010).
If I am not wrong, the above papers means that humans follow an entirely clinal pattern of genetic variance, and even the clusters identified in the Rosenberg study are an artifact of IBD.
I will cite Kevin here, as he explains the 2nd point pretty well:
https://twitter.com/itsbirdemic/status/1226212010255409154
Further analyses revealed even stronger geographic patterns or ‘clines’ (see Glossary): genetic distance between populations increased with geographic distance at both continental and global scales [5,6], which is characteristic of so-called ‘isolation by distance’ (IBD) [7] models.
So it seems to be almost (if not) entirely a clinal world, without any real clusters.
More after your reply, I was linked to 2 additional papers but want to keep it short. And yes these papers were linked to me from the geneticist.
Yes. Perhaps that just consisted of pulling the European cluster towards the midpoint? Presumably there were ancestral European populations (e.g. ancient tribes in Britain?) which were even further away from Africans before more modern transportation increased gene flow.
Remember that population genetics is under tension from isolation producing differences and mixing muting those differences. And this is all happening concurrent with selection.
You say that like it is a feature. To my mind all you said there is how biased he is.
How about more citing and less talking about how you could do so? To preempt some of the less useful conversations.
– No need to talk about the false dichotomy of IBD vs. other explanations. As I discuss below, what is important is that the differences exist.
– Sharing recent ancestry is pretty much given. What matters is the scope of the remaining differences.
– When “disagreeing with” clusters (what does that even mean?) focus on the actual data, not the causes.
If you do care to introduce specific arguments of his, how about doing so in individual comments? This would make it easier to track the progress of each individual argument.
Please include links.
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000500
This is one of the more interesting papers you have referenced.
One thing I think Coop has neglected to consider adequately is the possibility (prevalence) of balancing selection (“balanc” appears in his paper only in the title of one of his references).
https://en.wikipedia.org/wiki/Balancing_selection
That is a strange omission for as expert a geneticist as he is. Consider the sickle cell allele. The frequency differences never become that large because the homozygous recessive case causes disease.
I suppose that is partly covered (implicitly) in this excerpt. I think this makes clear the abstract oversimplifies things in a way your argument depends on.
We propose below that even if positive selection is common in the genome, strong selection that drives new mutations rapidly to fixation appears to be rare. Our results also argue against a strong form of adaptation in local populations by very large allele frequency shifts at individual loci. However, our data do not preclude a weaker level of adaptive tuning: i.e., modest frequency changes may often occur in response to local conditions [23],[24],[52]. Indeed, it is still possible that small frequency shifts at multiple loci could allow populations to effectively adapt to local conditions even in the absence of large frequency changes at individual loci.
Contrast that to your summary of Coop: “Selection has not acted on that many traits”
I think it is clear he is not asserting that. I am trying to decide whether your misleading summaries are due to ignorance (not reading and understanding the papers) or agenda (of course, both is always an option, I can think past false dichotomies). BTW, when you do things like that and then just move on to another (usually bad as well) argument when called on it, that’s a Gish gallop.
Regarding evidence for IQ selection, two points:
– Do you sincerely think IQ has not been selected for? If not then it is clear it is just a matter of finding the evidence.
– I think the presence of significantly differentiated SNPs (discussed elsewhere) serves as evidence.
Do you have any idea how tedious your vague “appeals to complexity” are? If you think I have been overly simplistic about something then call it out. Otherwise just be quiet about what is “often assumed.” It is not germane to our conversation.
So you don’t care that you can’t put a finger on where differentiation actually happened. Rather inconsistent with your demands for objective splits in the present. I’m not even sure what the rest of that paragraph means. But I am pretty sure it’s not worth the effort to understand.
How many times do I have to say I consider IBD a cause of race? Why the differences are present matters much less than that they ARE present.
So you are retracting your earlier agreement with my statement?
At this point you are looking like an insincere intellectual lightweight who is serving as a mouthpiece for someone who is only slightly better informed and afraid to come here and debate for himself.
From the paper the percent variance explained for the first three global PCs is 19.5%, 5.01%, and 3.5%. That makes clear how much the non/African split dominates things. Within Africa the percent variance explained for the first three PCs is 10.8%, 6.1%, and 4.9%. Actually, their full explanations of these are interesting, so:Back to you.Lee actually looks at this some (you have read the paper, right? if not go do that and stop wasting my time). A sample: "relative to other genes, genes near our lead SNPs are overwhelmingly enriched for expression in the central nervous system"
Other GWAS make more of an attempt to look at causality. Like the one I linked just above in comment 126 (referencing tissue types). Why do you keep raising issues I have already addressed?Then his analysis is wrong somehow, because we see that those variants do differ between populations in reality. Piffer's work using Lee's EDU PGS shows that quite clearly. You can argue about whether it is OK to use the PGS between populations to show phenotypes, but I don't think it is arguable that Piffer's PGS results show the frequency variation. Would you be more convinced if we looked at the distribution of particular variants? That is easy to do with GGV
https://popgen.uchicago.edu/ggv/?data=%221000genomes%22&chr=1&pos=222087833
You might take a look at rs61734410 mentioned in Lee's paper and compare the frequencies in East Asia to elsewhere.
I list some more SNPs in this comment:
https://www.unz.com/jthompson/the-worlds-iq-86/?showcomments#comment-2071349
Or you can do the heavy lifting yourself and go look at Lee's list.
I do not think you will reply but just for consistency I am replying to the points I did not earlier.
First, regarding the clusters from the HGDP etc studies, here is an article from my own field:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3941216/pdf/cshperspect-DIV-a021238.pdf
How these criteria reflect real history as well as the analysis itself may vary with the software
program used in the admixture analysis, and each program has its own assumptions and
methods, which can affect the results. For example, the investigators of the original modern
admixture program called STRUCTURE (Pritchard et al. 2000) clearly provide all of the appropriate caveats, in clear terms, and most importantly the subjective judgments required in interpretation and that the program is designed to estimate admixture history even when admixture is an appropriate way to view what actually happened (if that is even known).
However, most nonshared variants will only be found in some individuals in a purported race’s geographic homeland. That might seem to imply rather strangely that, depending on how definitions are operationalized, members of a purported race would not have all
of its defining alleles! This shows how what one chooses to sample can affect or even predetermine the results. That is not supposed to happen in science.
It is too long to cite here, but do take a look at their simulations in pages 10-12 as they show how artificial clusters are.
More on PCAs: https://www.genetics.org/content/211/1/289.abstract that also shows how assumptions on Fst can distort detection of selection etc that studies like Lee et al use:
“It is common to describe variation along the genome of simple statistics such as FST and to interpret the results in terms of the action of selection (e.g., Turner et al. 2005;
Ellegren et al. 2012). However, a given pattern (e.g., valleys of FST) can be caused by more than one biological process (Cruickshank and Hahn 2014; Burri et al. 2015), which in retrospect is unsurprising given that we are using a single statistic to describe a complex process. It is also common to use methods such as PCA to visualize large-scale patterns in mean genome-wide relatedness. In this paper, we show if and how patterns of mean relatedness vary systematically along the genome, in a way particularly suited to large samples from geographically distributed populations. Geographic population structure sets the stage by establishing background patterns of relatedness, our method then describes how this structure is affected by selection and other factors.
The method is descriptive: it does not aim to identify outlier loci, but rather to describe larger-scale variation shared by many parts of the genome and give clues about the source of
this variation.”