Tag Archives: heritability

Most of the genome is additive

17 Friday Feb 2023

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There seems to be a belief among some in the comment section that genetic effects are not (primarily) additive. By additive, we mean that by adding the gene, we will add to your phenotype; for example Steve Hsu estimates that replacing 100 negative height variants in your genome with 100 positive ones will add a few inches of height. That’s not to say that everyone with a given genotype will have the same phenotype regardless of environment, but rather it’s to say that good environments combine with good genes in an additive way; like a rising tide that lifts all boats without changing their relative heights.

However some are obsessed with Gene X environment interactions. That is gene A might add 1 inch if you’re in China but it will subtract 1 inch if you’re in Brazil. I don’t deny that such interactions exist. For example the Tarahumara of the Mexican highlands had very little exposure to agriculture and thus never evolved an ability to process refined carbs. So in their native lands, their genetics adds very little fat compared to whites reared in the same environment, but when they live in the United States, it adds hundreds of pounds of fat compared to American whites. So it’s not a case of a rising tide lifting all boats without changing their relative heights. In this case the rising tide (U.S. diet) lifts Tarahumara weight several times more than it lifts white weight. Tarahumara go from equal or maybe even leaner than whites when both races are raised in the wild, to several times fatter when both races are raised in a modern industrial society.

There are also gene X gene interactions (epistasis) where the effect of a given gene depends on other genes it its nexus. An obvious example is eye colour where having an allele for blue eyes only causes blue eyes when combined with another allele for blue eyes, but results in brown eyes when combined with a brown eyed allele.

These examples notwithstanding, many human traits, especially complex polygenic traits, are overwhelmingly additive. An obvious example is black people have darker skin and kinkier hair than white people, regardless of whether the two races are raised in America, Europe, Africa, China, or even Mars! There is no genes X environment interactions that alters that ranking.

People with Y chromosomes (on average) grow up to be much taller, stronger, faster, and hairier than women, regardless of whether they’re raised in India or Britain, so no gene X environment interaction. And regardless of whether they’re South Asian, white, Bantu, Pygmy, Dutch or Downs syndrome, so no gene X gene interaction either.

During the 20th century, the heights of both men and women increased dramatically all over the developed World, but that man > woman height gap remained similar. Again, the Y chromosome is an additive constant independent of what the environment adds. Similarly, ethnic differences in IQ have held constant in the United States over the 20th century, even though the average IQ of all races has increased quite a bit (see the Flynn effect).

People with a third chromosome on the 21st pair tend to be 50 IQ points lower and many inches shorter than their normal peers, regardless of race or continent, so again no interactions. Only additive independent effects.

In fact so independent are the effects of certain genes that they have similar effects on genomes and environments as disparate as humans living in the city and mice running through the grass. The FOXP2 gene is associated with language in humans. Humans with impaired FOXP2 genes struggle with words, syllables and sounds.

So what happens when you put the human version of FOXP2 in mice?

“There seems to be a change in vocalization — they squeak in a different way,” observed Nobel Prize winning geneticist Svante Paabo.

If the same gene can add vocalization skills to creatures separated by 65 million years of evolution, don’t tell me genes don’t have additive effects.

In similar experiments, scientists took the glowing gene from a species of jellyfish living in the ocean.

They found it had the same independent effect on everything from sheeps and rabbits living in fields to monkeys swinging from trees. Can’t wait for the first glowing person!

If genes can add the same effects across wildly different genomes in completely different environments, then surely they can be additive across different kinds of people living in our increasingly homogeneous global village.

Thoughts on Robert Sapolsky

15 Sunday Nov 2020

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I’ve long argued that the higher your IQ, the less likely you are to believe in God and it often takes an extra high IQ to reject religion when you were raised in a religious home. The brilliant Robert Sapolsky (who graduated summa cum laude from Harvard University) is a great example. Despite being raised Orthodox Jewish, he achieved secularism by his early teens, which evolved into atheism, and eventually utter atheism. My own unpublished research suggests that creationists average about 15 IQ points lower than non-theists. Extrapolating from here, it would be interesting if agnostics (like me) are less intelligent (on average) than atheists who are less intelligent than utter atheists but I don’t know if the relationship is quite that linear.

I’ve also long argued that the higher your IQ, the less racist you are and Sapolsky is also very non-racist. Alt-right commenters like “Philosopher” will think “he’s just pretending to be non-racist to manipulate gullible goyim into race mixing so they’ll be easier for Jews to dominate” but in fact we see that he is anti-racist even when his own ethnic interests are on the line, stating:

We humans are like most other social primates in that we very quickly, very unconsciously, very automatically tend to divide the world into “us” and “them”…I grew up as an Orthodox Jew, which was the religiosity that I broke away from. Now I am part of the way-too-small community of Jews who are anti-Zionist. It’s a little bit horrifying that among American Jews, 99 percent of the time, you’re finding people whose views are very different from my wife’s and mine. We’re not fans of what has been done in Palestine over the last 70 years.

This shows his non-racism is not an act, but a genuine product of high IQ. The fact that the negative correlation between IQ and racism might exist even within the Jewish community suggests the correlation is largely causal, and not merely an artifact of high IQ Westerners being brainwashed by liberal propaganda. Although intelligence is the ability to adapt, being too smart is genetically maladaptive in dominant races because the high IQ are abstract enough to pursue moral interests which typically conflict with the dominant group’s genetic interests.

Sapolsky is an excellent lecturer and I especially enjoyed his talk on behavioral genetics. He thinks classical twin studies where heritability = 2(MZ twins raised together corrrelation – DZ twins raised together) overesitmate heritability because, like many liberals, he thinks MZ twins raised together are not only more genetically similar than DZ twins raised together, but environmentally more similar (so the correlation difference can not be exclusively credited to genes).

He’s also skeptical that the MZ twins raised apart correlation = heritability because even separated twins may have correlated environments.

He alludes to an idea I never considered that would seem to solve both those problems:

Heritability = 2(MZ twins raised apart correlation – DZ twins raised apart correlation).

Has anyone ever calculated this?

Brain organoid research could teach us a lot about IQ

21 Thursday May 2020

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One way psychologists estimate IQ heritability (the percentage of variation in IQ linked to variation in DNA) is by correlating the IQs of monozygotic (MZ) twins raised apart. The higher the correlation, the more genetic IQ is thought to be.

However skeptics argue that because MZ twins raised apart still shared the same womb, and still grow up in the same country and sometimes the same town, the high correlation doesn’t prove the genetic effects are independent of environment (maybe the same genotype that increases IQ in the U.S. would decrease it Japan, but we’ll never know if virtually all the twins raised “apart” are still raised in the same country).

As commenter “Mugabe” suggested, the ideal study would have genetic clones separated at conception and gestated and raised by random women all over the developed World, but such a study would be unethical. And even if such a study were possible, and even if it showed strong independent genetic effects, the nature of these effects would remain mysterious. Does DNA directly cause IQ (i.e. coding for bigger and more efficient brains), or does it do so indirectly (i.e. causing us to stay in school longer, where we learn how to think). The problem with even the best designed study of MZ twins separated into random environments is that only the starting environment is random. As we grow old, we select environments that fit our DNA, and although the effects of such environments are counted as genetic effects (since our genes made us choose those environments) they are actually gene-environment feedback loops.

But what if it were possible to clone just our brains, and these cloned brains were reared in environments completely alien to anything we have experienced. You grew up in a nice middle class family, and your cloned brain grows up in a petri dish, where its environment was 100% controlled with no gene-environment feedback loop.

image found here

Then we could be sure that any cognitive correlation between us and our cloned brains was not only an independent genetic effect, but a direct one to boot.

It sounds like science fiction, but something similar is actually happening in the lab of Alysson Muotri, a biologist at the University of California, San Diego. Muotri takes skin cells from volunteers, turns them into stem cells, and then makes them grow into tiny pinhead sized balls of brain tissue called organoids.

Of course these organoids are way too tiny to be considered cloned brains, but they are complex enough to make brain waves. And Muotri has already found that cognitively impaired populations have cells that produce underdeveloped brain organoids in the petri dish. For example brain organoids derived from autistic people had about a 50% reduction in synaptogenesis.

Muotri also decided to study Neanderthal brain organoids. Since it’s not possible to get cells from Neanderthals, he edited modern human DNA. Of the 20,000 protein coding genes, only 61 differ between us and them, and of these, only four are highly expressed in the brain so by editing just these four genes, he was able to produce Neanderthalized organoids, or Neanderoids as he calls them. Modern humans had far more spherical skulls than Neanderthals so it’s interesting that our brain organoids are spherical, while theirs look like popcorn.

popcorn

Muotri notes that like the autistic brain organoids, the Neanderoids have a 50% reduction in synaptogenesis. Neanderoids also show 65% to 75% reductions in firing rate and activity level per neuron per minute. Muotri thinks this may help explain why it took them several hundred thousand years to progress from simple stone tools to, well, simple stone tools. By contrast, in just the last 50,000 years we jumped from simple stone tools to the internet, genetic engineering and traveling to the moon.

image from Muotri’s talk comparing our rate of cultural progress to Neanderthals’

So clearly brain organoids are very good at identifying cognitively impaired populations, but can they measure normal variation in human intelligence?

Muotri could greatly advance our understanding of behavioral genetics if he made brain organoids of a representative sample of Americans of known IQ scores, and then correlated the synaptogenesis, neuron activity level and firing rate of the organoids with the tested IQs of the people from whom they were derived. Perhaps a carefully weighted composite score of all three measures would give the best prediction of IQ, and perhaps such a formula could allow us to estimate how Neanderthal’s would score on IQ tests (if they were reared in our society).

If it’s too difficult to get a representative sample of Americans and test their IQs, he could simply have students at his university donate their cells, and then correlate their brain organoid scores with their SAT scores. Would there be statistically significant differences in the brain organoids of people who score a perfect 1600 on the SAT compared to those who score 1400 compared to those who score 1200 compared to those who score 1000?

Muotri is also trying to teach the brain organoids how to control a robotic body. The speed with which they learn might be considered a low level IQ test. So imagine taking a conventional intelligence test like the Wechsler Adult Intelligence Scale (WAIS) or the SAT, while your mini-brain, raised in a petri dish is taking its own IQ test (learning to control its robotic body). This could be the 21st century version of studies where identical twins raised apart have their IQs correlated. If your score on a conventional intelligence test predicts the speed with which your brain organoid learns to control its robotic body, then that proves IQ tests are measuring a genetic property of the brain that is completely independent from social class and culture because environment is perfectly controlled in the petri dish.

Perhaps in the future instead of universities testing candidates on the SAT, they’ll just test the student’s brain organoids instead to eliminate the cultural bias some think confounds the SAT. For there’s no culture in the petri dish (aside from bacteria culture :-)).

When a prosecutor suspects a murderer is faking his low score on the WAIS to avoid execution (because it’s illegal to execute people with IQs below 70 in some states) he could insist on testing the murderer’s brain organoid instead (since they can’t fake low scores-as far as we know).

On the other hand brain organoids might prove that normal variation in IQ is nowhere near as genetic or biological as its proponents think. I find it fascinating that just four brain genes separating modern humans from Neanderthals produced such dramatic differences in brain organoids. That implies each gene must have huge effects. That’s not at all consistent with research on normal IQ variation among modern humans, which estimates that some 10,000 genomic variants are involved, each one affecting IQ by only a fraction of a point. It’s also possible that brain organoids showcase too early a stage of brain development to correlate with the higher abstract abilities measured by IQ tests (for example infant development scales have weak correlations with adult IQ).

In the below video Muotri discusses his brain organoid research:

Why does shared environment affect some IQ tests more than others?

04 Saturday Apr 2020

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Using twin studies, scientists divide phenotypic variation into three categories: DNA variation, shared environmental variation, and unshared environmental variation. Shared environment are all the experiences MZ twins reared together have in common (same upbringing, same schools, same womb) while unshared environment are all the experiences they don’t share (position within the womb, getting hit on the head, having an inspiring teacher).

The best estimate using massive datasets suggest that within Western democracies, DNA explains 41% of IQ variation at age 9, 55% at age 12, 66% at age 17, and 74% in adulthood. By contrast shared environment explains 33% at age 9, 18% at age 12, 16% at age 17, and 10% in adulthood (Bouchard 2013, figure 2). That leaves unshared environment explaining 26% of the variation at age 9, 27% at age 12, 19% at 17, and 16% in adulthood.

You don’t have to believe these associations are causal, but they are real. They’ve been more or less replicated using studies comparing (1) MZ twins with DZ twins, (2) MZ twins raised apart, (3) unrelated people reared in the same home. Although all of these methods depend of different assumptions, they all converge on the same conclusion: the predictive power of DNA skyrockets from childhood to adulthood while the predictive power of shared environment plummets. The same pattern (known as the Wilson effect) has also been observed for other phenotypes and in other species.

But why? Shouldn’t environment get more important as we age since experience has increasing time to accumulate? One theory is that more and more genes become active as we age. A more popular theory is that we select environments that maximize our genotype, so environment becomes just a magnifier of genes, not a causal force in its own right. So genetically smart people will stay in school and genetically strong people will lift weights and take steroids etc. People invest in where they’re more likely to be rewarded.

But here’s where things get really interesting. The Wilson effect behaves differently on different types of IQ tests. In his book Does your Family make you smarter? James Flynn notes that cognitive inequality increases from childhood to later adulthood (because good genes cause good environments and bad genes cause bad environments, the smart get smarter and the dumb get dumber, relative to the average person their age) but this pattern is much more pronounced on some tests than others.

Flynn describes three types of tests:

  • Type 1: Tests that show large family effects (shared environment) that decay slowly. This include tests involving vocabulary (define “rudimentary”), general knowledge (How old is the Earth?) verbal abstraction (how are a brain and a computer the same?) and social comprehension (why do you need a passport to travel?)
  • Type 2: Tests that show small family effects that decay fast. These include spatial manipulation (use these two triangles to make a square) and noticing incongruities (what’s missing or absurd in a picture of a common object or scene).
  • Type 3: Tests that show that large family effects that decay fast. These tests include clerical speed and arithmetic.

Flynn argues that type 1 tests involve skills that children learn from observing their parents talk, hence the large family effect. By contrast he says of type 2 tests:

Aside from the occasional jigsaw puzzle, they have no part in everyday life. Children never see their parents performing these cognitive tasks as part of normal behavior. Family effects are weak, even among preschoolers. Since these subtests match environment with genetic potential so young, they would be an ideal measure (for, say, 5-year-olds) of genes for intelligence.

From pages 53-54 of Does Your Family Make You Smarter? by James Flynn

In other words, Type 2 tests measure “novel problem solving”, while type 1 tests measure acquired abilities. A more provocative interpretation is type 2 tests measure real intelligence, while type 1 just measure knowledge and experience. This is the age-old distinction between aptitude tests vs achievement tests, culture fair vs culture loaded, fluid vs crystallized.

And yet Flynn largely rejects Cattell-Horn-Carroll’s theory that fluid ability (novel problem solving) is invested to acquire crystallized ability (accumulated knowledge) writing:

…fluid skill is just as heavily influenced by family environment as the most malleable crystallized skill (vocabulary) and therefore, neither skill deserves to be called an investment and the other a dividend.

From page 132 of Does Your Family Make You Smarter? by James Flynn

Flynn of course is referring to the greatest irony in the history of psychometrics and the biggest mistake of Arthur Jensen’s career: the Raven Progressive Matrices (long worshiped by Jensen and Jensenistas as the most culture fair measure of pure intelligence ever invented) is a type 1 test!

Which of the 8 choices completes the above pattern? Image from  from Carpenter, P., Just, M., & Shell, P. (1990, July)

But let’s not throw the baby out with the bath water. There’s no need to abandon CHC investment theory just because a major test got mischaracterized. But at the same time, it doesn’t feel right to reclassify the Raven as a crystallized test, Research is needed to understand why the Raven is so culturally sensitive when it superficially looks like a measure of novel problem solving. Is it measuring some kind of implicit crystallized knowledge we’re not conscious of like being familiar with patterns, columns and rows and reasoning through the process of elimination, or are the family effects on the non-cognitive part of the test (having the motivation to persist and concentrate on such an abstract task). Flynn argues that the brain is like a muscle, but if so, the Raven is an exercise most have never done before, so why isn’t it a type 2 test?

Flynn might argue that if your family helped you with abstract problems in algebra or had philosophical discussions about hypothetical concepts, you’ve been exercising for the Raven all your life, but this seems like a bit of a stretch. All the research shows that cognitive training has narrow transfer (i.e. practicing chess will only make you slightly better at checkers, and not at all better at scrabble) though perhaps the Raven’s uniquely abstract (general) nature allows it to slightly buck this trend.