Hello There, Guest!  

[OBG] Estimating the genotypic IQ of populations and assessing

#1
Principal components analysis on allele frequencies for 14 and 50 populations (from 1K Genomes and ALFRED databases) produced a factor accounting for over half of the variance, which indicates selection pressure on intelligence or genotypic IQ. Very high correlations between this factor and phenotypic IQ, educational achievement were observed (r>0.8), also after partialling out GDP and the Human Development Index. Regression analysis was used to estimate a genotypic (predicted) IQ also for populations with missing data for phenotypic IQ. Socio-economic indicators (GDP and Human Development Index) failed to predict residuals, not providing evidence for the effects of environmental factors on intelligence.
Another analysis revealed that the relationship between IQ and the genotypic factor was not mediated by race, implying that it exists at a finer resolution, a finding which in turn suggests selective pressures postdating sub-continental population splits.
Genotypic height and IQ were inversely correlated but this correlation was mostly mediated by race. In at least two cases (Native Americans vs East Asians and Africans vs Papuans) genetic distance inferred from evolutionarily neutral genetic markers contrasts markedly with the resemblance observed for IQ and height increasing alleles.
A principal component analysis on a random sample of 20 SNPs revealed two factors representing genetic relatedness due to migrations.However, the correlation between IQ and the intelligence PC was not mediated by them. In fact, the intelligence PC emerged as an even stronger predictor of IQ after entering the “migratory” PCs in a regression, indicating that it represents selection pressure instead of migrational effects.
Finally, some observations on the high IQ of Mongoloid people are made which lend support to the “cold winters theory” on the evolution of intelligence.


Attached Files
.docx   GenotypicIQ 1008.docx (Size: 39.12 KB / Downloads: 364)
.zip   dataset.zip (Size: 17.27 KB / Downloads: 397)
 Reply
#2
This line of research should be a top priority, and I hope its author will target a first-tier journal in the near future.

I have one serious criticism. The choice of IQ-increasing alleles should be as impartial as possible. Ideally, the author should use a list of alleles that someone else has drawn up. I understand his reasons for choosing certain alleles and excluding others, but he may inadvertently be exposing himself to attack. How different would the picture be if he simply included all alleles that are known to increase IQ?

I still hold to my view that the author seriously misunderstands the dynamics of sexual selection. Sexual selection is not driven by preferences alone. Preferences translate into sexual selection only if your sex is in limited supply.

"This finding (if replicated) would yield support to the “cold winters theory”, which posits that the higher IQ of East Asians originated in a region roughly corresponding to modern day Mongolia and Manchuria, characterized by extremely low winters temperatures and then spread to the south of China and Japan through migrational waves."

I agree that northern sub-Arctic environments were a key selection pressure in raising IQ among early modern humans, specifically the need to develop technologies for storage, meat refrigeration, and heat conservation, and more generally the need to find ways to collect unpredictable and widely dispersed resources. This IQ increase, however, would have taken place among all northern Eurasians of the last ice age, i.e., the ancestors of present-day Europeans, East Asians, and Amerindians. The relatively higher mean IQ of East Asians is probably a much more recent development that occurred during historic times. Ron Unz is the best source on this topic:

Unz, R. (2013). How Social Darwinism made modern China, The American Conservative, March 11

http://www.theamericanconservative.com/a...china-248/

It would be interesting to determine the IQ of present-day indigenous Siberians.
 Reply
#3
It's an excellent point you have specified the difference in between and within-group difference. Lot of people in blogs/forums don't truly know the difference. Say, you have africans low in characteristics X, asians high, and whites in the middle, this pattern follows IQ levels, and then, they conclude it must also be the case within populations (that is, high IQ correlate positively with characteristic X). Just like some discussions I have been through regarding the negative relationship between income inequality and income mobility. Most people believe that if the relationship is true cross-nationally, it must also be true within countries. That's false, as I have seen, there is no resemblance in the trend over time in these two variables in the US and Canada, for example.

Below, in bold, are my concerns concerning typos (you can try CTRL+F for search in the sentences quoted below) :

Quote:A principal component analysis on a random sample of 20 SNPs revealed two factors representing genetic relatedness due to migrations.However, the correlation between IQ and

c) test the environmentalist hypothesis that residuals (countries whose estimated IQs are lower or higher than predicted by their genetic factor scores) are explained by socioeconomic factors.Finally: d) to shed

Recently, a new study has replicated the positive effect of these top three SNPs rs9320913, rs11584700 and rs4851266 on mathematics and reading performance in an independent sample of school children (Ward et al., 2014).Intelligence is a good predictor

Predicted IQ and standardized residuals (Z_RES)were also calculated

Seven groups were created (0=African; 1=Middle Eastern; 2=European; 3= Western Asia; 4= East Asian; 5=Native American; 6:South East Asian

A significant model emerged (F4,14= 15.77, p=0.000; (R²= .818; Adjusted R²= 0.767).Only the genotypic IQ factor was a significant predictor of IQ.

This between-groups pattern contrasts with the withingroup pattern, where IQ is slightly higher on average in taller people than in shorter people

1)The lower IQ of Sub-Saharan Africans

the genotypic IQ factor emerged as a significant independent predictor of IQ in both datasets (ALFRED and 1000 Genomes),independently

Now, some comments :

Quote:A relatively well-known study (Chabris et al., 2012) claimed that, although a number of candidate genes had been reported to be associated with intelligence, the effect sizes were small and almost none of the findings had been replicated.

The authors here said that it is certainly due to not having enough sample, i.e., problem of insufficient power.

Quote:Group was a significant predictor in the model (p= 0.000) but the IQ PC was not (p= 0.768) (table 7) indicating that the inverse correlation between genotypic height and IQ is mediated by racial origin.

It's a perfect illustration of why I dislike virtually all applications of ANOVA-like stats. Because the effect size is not reported. Only the p-value. But if you use SPSS, normall, the (partial) eta-squared should be also available in the input, right ? Can you report it ?

Concerning table 13, the unstandardized coeff for PC1 is -2.594, which is the IQ loss for one unit increase in PC1.
 Reply
#4
(2014-Aug-12, 02:17:54)Peter Frost Wrote: This line of research should be a top priority, and I hope its author will target a first-tier journal in the near future.


Well, if he wants to push this metajournal, then perhaps publishing everything here is a good idea. I try to publish anything relevant in these journals for the reason that I want to set a good example.

Quote:I have one serious criticism. The choice of IQ-increasing alleles should be as impartial as possible. Ideally, the author should use a list of alleles that someone else has drawn up. I understand his reasons for choosing certain alleles and excluding others, but he may inadvertently be exposing himself to attack. How different would the picture be if he simply included all alleles that are known to increase IQ?

For statistical reasons, one cannot easily use all of them. The number of cases (populations) is too small. Each SNP is a variable. Generally, it is bad if the var-case ratio is <1, see the discussion in my paper in review about factor analysis.
 Reply
#5
Quote:I have one serious criticism. The choice of IQ-increasing alleles should be as impartial as possible. Ideally, the author should use a list of alleles that someone else has drawn up. I understand his reasons for choosing certain alleles and excluding others, but he may inadvertently be exposing himself to attack. How different would the picture be if he simply included all alleles that are known to increase IQ?
I did include all the alleles that are known to increase IQ. When I included more alleles I was criticized for also including those that were not replicated. Now that I include only those that were replicated, I am criticized for excluding the possible false positives.
The top 3 alleles from Rietvald et al. were replicated by Ward et al. and are the only alleles whose effect has been replicated, plus the Benyamin et al.'s rs236330.
Adding more alleles (the likely false positives) would just decrease case (populations) to variable (SNPs) ratio. A way round this problem would be to create lots of polygenic scores and then factor analyze them, like I did for my height data set. However, the height alleles have much smaller p values than the alleles associated with cognition because they're based on much bigger samples. I am afraid that the IQ alleles comprise so many false positives that it's better just to stick to the alleles with "known effect" (those that were replicated), also avoiding the criticism that I've not used replicated alleles!
So now my choice of alleles is as impartial as possible because there are no other alleles whose effect on IQ has been replicated. The criterion of choice (replicated positive effect) is as sound and impartial as possible. A critical reviewer wanting to object to the impartiality of my choice would have to point out other alleles with replicated effects, that I excluded from the analysis. But since such critic will deny there are other replicated alleles, the logic of his entire argument falls apart here.
Quote:I still hold to my view that the author seriously misunderstands the dynamics of sexual selection. Sexual selection is not driven by preferences alone. Preferences translate into sexual selection only if your sex is in limited supply.
This is not the place to begin a long discussion about sexual selection, which is only a minor digression in my paper and away from the central theme. The most authoritative source on sexual selection I consulted (Andersson, 1994) supports my view "Sexual selection can, however, work also in monogamous species if the sex ratio is skewed, or if mates differ in quality (Darwin, 1871; Fisher, 1958) For example, among female birds, those in best condition are ready to breed first in the season, and so will have most time for raising young, hence producing most offspring. The first males to mate are therefore likely to get the most productive females. In addition, variation in mate quality might also affect the partner's survival. The better a parent provides food and guards against predators, the better its family should fare, including its mate. Such effects should augment the advantage of having a high-quality mate in species with biparental care. Traits that improve the ability to compete over mates should therefore be favored in monogamous as well as polygynous species" (Andersson, 1994, pp.9-10). If you want to continue the discussion on sexual selection I invite you to email me.
Quote:This IQ increase, however, would have taken place among all northern Eurasians of the last ice age, i.e., the ancestors of present-day Europeans, East Asians, and Amerindians. The relatively higher mean IQ of East Asians is probably a much more recent development that occurred during historic times.
It would be interesting to determine the IQ of present-day indigenous Siberians.

I never claimed that the IQ increase happened ONLY during the last ice age. That's why I carried out the within-race analysis, and I found positive results (i.e. selection continued after racial splits, at a sub-continental level). So yes, my results support your contention that the higher IQ of East Asians could be a recent phenomenon.
 Reply
#6
Thanks Meng Hu, I'll correct these typos. Glad you appreciate my distinction between within-and between populations. Many people are too simple-minded to appreciate it.
Quote:
Quote:A relatively well-known study (Chabris et al., 2012) claimed that, although a number of candidate genes had been reported to be associated with intelligence, the effect sizes were small and almost none of the findings had been replicated.

The authors here said that it is certainly due to not having enough sample, i.e., problem of insufficient power.

The problem is that the Chabris et al. paper is widely cited by IQ genes denialists (in blogs or even by hawkish reviewers) as "evidence" that no alleles are associated with IQ. My point is that it's outdated as it's been made redundant by more recent meta-analyses, which used bigger samples and it cannot be considered evidence (as many people do) that no alleles are associated with IQ.

Quote:It's a perfect illustration of why I dislike virtually all applications of ANOVA-like stats. Because the effect size is not reported. Only the p-value. But if you use SPSS, normall, the (partial) eta-squared should be also available in the input, right ? Can you report it ?
The effect size is reported in table 4, as Type III sum of squares (which includes interaction effects). I do not think the partial Beta squared is available for this type of analysis. http://support.sas.com/documentation/cdl...ect031.htm
Quote:Concerning table 13, the unstandardized coeff for PC1 is -2.594, which is the IQ loss for one unit increase in PC1.

Yes, the p value is 0.161. It's reported in the table but since it's not very significant I didn't give it much space in the discussion. However I specified that genetic distance from Africa accounts for part of the IQ differentials, albeit this effect is much smaller in comparison to the IQ PC (extracted from the 4 SNPs).
I also found a mistake I had made in the discussion "However, the higher genotypic score of African Americans compared to sub-Saharan Africans (77 vs 93)". It's 77vs73.
I am also puzzled by why I get only 77 as genotypic IQ for African Americans, whereas the measured IQ is 85. A possibility is that the 1K genome sample consists of more "pure" African Americans, with lower White admixture. They're classified as "ASW", Blacks from SouthWestern US...I guess they less mixed with Whites than Blacks living in the north or the SE? Or it could be that the African American phenotypic IQ is increased by outbreeding.
 Reply
#7
Or that AA IQ is boosted by being in a country mostly run by higher g people. Surely, the US has a better environment for AA's than AA's would have if they were in the US by themselves. This hypothesis goes against the usual assumption that the environment part of the explanation of the AA-white IQ difference increases the difference rather than making it smaller.
 Reply
#8
Emil,

I believe in OBJ, but it will be some time before we get it up to first-tier status. This is a crucial area of research, and its findings should get as much exposure as possible. If the author can replicate his findings with as many as fifty IQ-enhancing alleles, I would strongly advise him to submit to a major journal.

Duxide,

I understand your situation. Ideally, the list of IQ-enhancing alleles should be drawn up by someone else. This problem will hopefully resolve itself as more people become drawn into this area of research.

With respect to the "cold winters theory", it might be advisable to cite authors outside the community of IQ researchers. Several anthropologists have studied the correlation between latitude and technological complexity among hunter-gatherers. Two good references would be:

Hoffecker, J.F. (2002). Desolate Landscapes. Ice-Age Settlement in Eastern Europe. New Brunswick: Rutgers University Press. p. 10

Zvelebil, M. (2009). Hunters in Transition: Mesolithic Societies of Temperate Eurasia and Their Transition to Farming, Cambridge University Press. p. 170

With respect to the issue of sexual selection, I cannot comply with your request to communicate with you offline. Any communication between a reviewer and an author must be available to all other reviewers. The review process must be as transparent as possible, for obvious reasons.

You're proposing a model of sexual selection where women are the limited resource because men are competing only for "high-quality women", i.e., women who are more fertile or who have access to more resources. This is unlikely in a nomadic hunter-gatherer society where most women typically die before menopause and where individual accumulation and/or monopolization of resources is very difficult.

Your model is all the more unworkable because in non-tropical regions the operational sex ratio tends to be skewed towards a surplus of women on the mate market. This is partly because the cost of polygyny for men is higher and partly because hunting-related mortality tends to exceed food-gathering-related mortality in non-tropical environments.

I realize this is a minor point in your paper. So why not just drop it entirely? It's the sort of just-so reasoning that will make your paper seem less credible.

I'm sorry to be so critical, but that's my role as a reviewer. I would not be doing you a favor, or anyone else, by not telling you what I really think.
 Reply
#9
Quote:With respect to the issue of sexual selection, I cannot comply with your request to communicate with you offline. Any communication between a reviewer and an author must be available to all other reviewers. The review process must be as transparent as possible, for obvious reasons.

Yes and this is exactly why Emil and I set up this journal. This is the only journal that happens to allow open peer review, and I was one of the two creators because I firmly believe in open peer review. You seem to be inconsistent here because you're praising open peer review system and criticizing the review of traditional journals which is not transparent at all, happening with anonymous reviewers and mediated by an editor which can even decide that the author has no right of reply to reviewers' comments! Why should I publish in such a dumb journal(by your suggestion I should publish in a top-tier journal with corrupt and evil review system)?When you submit papers to other journals the review system is closed and none but the author can see the reviews.
The reason I asked you to talk about sexual selection via email is because my paper is not at all about sexual selection and it's not proper to talk about it here, given it's such a minor point. In the whole paper I mentioned sexual selection only once and in less than a sentence , where I even admitted that was a speculation and even provided the alternative hypothesis of cold winters("It can only be speculated that this trade-off was due to sexual selection (for brawny vs brainy males) or selective pressure due to climate, favoring shorter limbs (via Allen’s rule) and bigger brains in colder environments (Piffer, 2014)" , yet from your comment it could look like my paper is all or mostly about sexual selection, and this has the negative effect of misleading other readers.
You seem a bit keen to continue the discussion on sexual selection from my previous paper (which is published) and if you want to do so (but not via email) please do that on the post-review discussion there but this thread is not the right place for left-overs from other papers. Mine was just a polite way of saying that I will not respond to your criticisms on sexual selection (the author cannot be forced to respond to all the reviewers' comments) if you post them on this thread, because it risks directing the whole discussion away from the focus of my study. Would have it been better if I had said nothing, so that you'd have kept writing about sexual selection and I'd have refused to reply without even justifying my behavior? I adopted a more honest approach and I decided to state bluntly that since I do not regard this thread a proper place for a discussion on sexual selection, I will not join such a discussion here. So I'll say this again in clearer terms: if you want to discuss about this, please do it via email or on another thread -unless you just want to write knowing I'll not reply to your criticisms - because I do not deem this a sufficiently relevant topic and as author I am exercising my right of not responding to all the criticisms.I was hoping you'd understand this before, but you're forcing me to be brutally honest.
Quote:I realize this is a minor point in your paper. So why not just drop it entirely? It's the sort of just-so reasoning that will make your paper seem less credible.
You are being critical when it's totally unnecessary because you're making a big deal out of a sentence where I cite a previous paper of mine (am I not even allowed to cite another work??)and I just admit it's a speculation and I even provide an alternative hypothesis!In this paper I just showed there is a negative correlation between genotypic IQ and height and my aim is just to report these results, not to discuss their evolutionary implications!That would go beyond the scope of this paper! I understand that you're very emotionally attached to sexual selection because it's your area of work, but it's a bit egocentric to want to draw the discussion on that topic just because it's so important for you, although it's irrelevant to the thesis of my paper. I cannot drop a comment just to please a reviewer. I know that this is probably gonna cost me your publication's approval (as you did for my previous paper, when you disappeared from the review).In that case, eventually other reviewers will be able to evaluate on their own whether your rejection of my paper (which oddly you keep wishing to see published on "top tier journals", instead of recommending publication here....Frankly I never heard of a reviewer that expresses his opinion on a paper submitted to a journal recommending publication on a different journal!! This struck me as utterly funny!) based on a non-existing issue is justified or not and consequently, if you were a fair judge of my work.

Edit 1: I think any reviewer (and especially those who show lack of comprehension and project it onto the author) would benefit from reading this: http://www.openpsych.net/forum/showthrea...40#pid1140

Edit 2: I think the properties of a bad review are fairly general and they repeat throughout the history of science, as this letter by Isaac Newton in response to a criticism by Hooke can be applied to many reviews, and highlights the same mistakes that PF (like Hooks) made:
"I shall now take a view of Mr Hooks Considerations on my theories. And those consist in ascribing an hypothesis to me which is not mine; in asserting an hypothesis which as to the principal parts of it is not against me; in granting the greatest part of my discourse if explicated by that hypothesis; and in denying some things the truth of which would have appeared by an experimental examination".
All these things, mr Frost, you've done with regards to my sexual selection hypothesis.

Edit 3: Your criticism to my sexual selection hypothesis is wrong. You keep assuming it depends on the sex ratio or a polygynous system but as the paragraph I cited said, this is unsupported by evolutionary theory.It's really distressing how you ignore or fail to understand even the simplest concepts. "In addition, variation in mate quality might also affect the partner's survival. The better a parent provides food and guards against predators, the better its family should fare, including its mate. Such effects should augment the advantage of having a high-quality mate in species with biparental care. Traits that improve the ability to compete over mates should therefore be favored in monogamous as well as polygynous species" (Andersson, 1994, pp.9-10). If you want to continue the discussion on sexual selection I invite you to email me." This, Sexual selection can, however, work also in monogamous species if the sex ratio is skewed, or if mates differ in quality". Which means that if mates differ in quality sexual selection can work (contrary to what you say) even if the sex ratio is not skewed! But again, I invite you to continue discussion of this issue, which is totally irrelevant to my paper, in a place other than this thread.

Edit 4: You also say "the list of IQ-enhancing alleles should be drawn up by someone else". I already said that there are only 4 IQ enhancing alleles whose effect has been replicated. If someone else drew them up, he'd get the same four. Until a few months ago everyone who criticized my work thought there were no replicated aleleles. Since then only the 3 Rietveld et al. alleleles have been replicated, so only these could be drawn up by someone else. Again, your criticism does not make sense.
 Reply
#10
Duxide,

"by your suggestion I should publish in a top-tier journal with corrupt and evil review system"

That is exactly my suggestion. Yes, life is unfair, but we only have one life to live, and the most sensible solution is to negotiate with life as best we can.

I believe that your findings deserve much more exposure than they are currently getting. Unfortunately, more exposure will be possible only through publication in a top-tier journal. I believe in OBG, but it will be many years before it gains the status of Nature Genetics or even Evolution and Human Behavior. This is how academia works. If you publish in obscure journals, people will assume your findings are obscure. Again, life is unfair, but one cannot take one's life back to a dealer and ask for a refund. We have to play the cards we're dealt.

You can increase your chances of publication by following a few basic rules:

- Don't wander off topic. The more you wander off topic, the greater the chances of writing something that will piss off one of the reviewers (or the editor). Sexual selection is one such topic. Many reviewers will dismiss any talk of sexual selection as total nonsense -- "Just-so stories." This kind of situation is unavoidable if sexual selection is the main topic of your paper. In your case, it isn't. You're creating needless problems for yourself.

- Don't cite non-experts. Richard Lynn is a fine man, but he is not an expert on technological complexity in hunter-gatherers.

- Anticipate criticisms. You've done this admirably.

Even if you do everything right, your chances of acceptance will never be greater than 50%. This is a difficult topic to write about, and many people will react angrily. But there is no fool-proof way of screening out angry reviewers. You're facing a deep-seated ideological prejudice that cannot be resolved through a different form of peer review.


"You also say "the list of IQ-enhancing alleles should be drawn up by someone else". I already said that there are only 4 IQ enhancing alleles whose effect has been replicated. If someone else drew them up, he'd get the same four."

Fine. I may be worried for no reason. I was just trying to anticipate a possible criticism.


"I never heard of a reviewer that expresses his opinion on a paper submitted to a journal recommending publication on a different journal!!"

I have. As a reviewer, I've often made that kind of comment. Please keep in mind that I'm not talking about the present paper under review. I'm saying that if you can increase the size of your dataset, you should consider publishing a subsequent paper in a top-tier journal. That's not an insult. That's a compliment.
 Reply
 
 
Forum Jump:

Users browsing this thread: 1 Guest(s)