When I am not feeling well I often watch Netflix, since my brain really operates at a lower level (passive, consumptive). Curiously I was recommended a Turkish series about the father of Osman (the founder of the Ottoman dynasty), Ertuğrul. I only watched a little bit of it, but it reminded me of the mini-series from the early 2000s around Attila. There are so many commonalities across the nearly one thousand years that separate the Ottomans and Attila, but it shouldn’t be surprising, as it is highly likely that some element of the Hunnic horde was Turkic in origin.
Though I spend a lot of time on this blog talking about Indo-Europeans, because they are a rather big deal, and, they are prehistoric, I think it is important to remember the Turks as well. The similarities are clear. Both groups began at one end of the great Eurasian steppe but swept repeatedly to the other end. Both were at least in part nomadic, and both integrated with other ethnic groups along with their expansions. But the Turks operated on the edges of, and within, history. We know, for example, the importance of Sogdians in playing the role of Greeks to their Romans.
There is a curious tendency, perhaps somewhat justified, of focusing on the Turks after their predominant conversion to Islam around the centuries of 1000 A.D. But Turkic customs and folkways persisted for many centuries, and continue down to the present in a relatively unadulterated form in places like Kyrgyzstan. In The Turks in World History the author recounts how a Cuman chief leading his host into battle against the Byzantines gave a cry that mimicked a wolf, and how his horde repeated it in en masse. This is a callback to the earliest legends of the origins of the Turks, which assert that they were birthed from a she-wolf, and lived as smiths among other peoples.
Probably the best treatment of their common ancestry is in The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia. Though genome-wide the predominant northeast Eurasian character of the original Turks is swamped out by the time one reaches Anatolia, there is still an enrichment of i.b.d. tracts even that far, indicating a lineal which stretched from Siberia down to the Middle East.
Anyone who first sees a map of Indo-European languages is often amazed and surprised by their expanse. How could premodern people be so expansive and widespread? And yet the Turks show exactly how such a thing could happen, and they expanded into a much more densely populated and civilized world than the Indo-Europeans.
One of the major insights of contemporary cognitive psychology is that a lot of human mental processes emerge from the intersection of lower level intuitions/models/instincts. The key is to remember that a lot of mental operations occur implicitly and rapidly, and we often construct ad hoc rationalizations after the fact (see The Enigma of Reason).
Because rationality is such a good talker many of us have deluded ourselves into thinking that instead of being a mouthpiece and a lawyer that gets us out of sticky situations, it’s actually calling the shots. No.
This comes to mind when thinking about issues that have been bubbling up in our society. A friend on Facebook who is an evolutionary anthropologist wondered about the context of Harvey Weinstein’s serial rapes. I think A Natural History of Rape: Biological Bases of Sexual Coercion get’s a bad rap because of the incendiary topic, but in this case, I think cognitive psychology yields a quicker and clearer answer. Weinstein is a very wealthy man, so if it was sex with nubile women he could have paid for high-priced escorts (and it seems he did on occasion). But cognitive psychology suggests that people crave “authenticity.” Weinstein’s targeting and abuse of women he knew professionally and personally clearly provided for him an addictive frisson that paying for sex wouldn’t have given him.
In other words, when it comes to deeply held beliefs people aren’t going to react in a straightforward manner to reason and logic. Don’t be surprised if they behave irrationally. If the irrationality is consistent across individuals there’s probably some deeper psychology you aren’t accounting for.
The problem of doctors’ salaries. The AMA licensing cartel is keeping the supply of medical services constrained. Yes, we need more doctors. But we need more non-doctors to be able to do things that only doctors can do right now.
On the other hand, medical doctors have on average $200,000 of educational debt when they graduate. The high debt load is probably in part because there is the assumption that they will be making between $200,000 and $400,000 per year (though with income tax rates, as well as malpractice insurance, remember their net take home is considerably less).
These sorts of structural features are why we can’t have nice things. I suspect most people agree that the American tax code should be reformed…but peoples’ choices have been made with deductions in mind!
We’re rolling out more shirts for DNAGeeks. Eight people have bough GNXP t-shirts. Would be curious to post a picture of someone wearing one of those. A little surprised, but the Evo-Devo t-shirts are selling well. Anyone have any ideas for something more pop-gen related?
I love maps [THE MAP IS FAKE!] which have more granularity than country vs. country comparisons. I really hate when people compare the USA to European countries. California alone is nearly as populous as Spain, which isn’t even a small European country.
The map to the left shows the areas of high GDP in South Asia, though resizing region by the size of the population would help give a better sense. The distinction between urban and rural is very stark in Bangladesh.
I predict Twitter will be clearly in a death spiral in a year. The proportion of highly polarized political chatter on my timeline keeps increasing, even though I’m not following anyone different. The vibrant years of “genomics twitter” seem to be a thing of the past.
when i was young i imagined that fundamentally the non-west would become like the west. now i see the west become like the non-west. #globalismIsABitch
The above tweet has gone somewhat viral. What did I mean above? The sort of thing in The End of History and the Last Man, that the terminal stable state of humanity would be post-materialist secular individualist liberalism. Though secularism seems to remain ascendant in the West, for now, the post-materialist individualism liberal project seems to be fraying. Instead of Western culture being a stand-in for global culture, it may be in the near future it will again be just another culture among cultures.
…Burials at Verteba Cave are largely commingled and secondary in nature. A total of 68 individual bone specimens were analyzed. Most of these specimens were found in association with well-defined Tripolye artifacts. We determined 28 mtDNA D-Loop (368 bp) sequences and defined 8 sequence types, belonging to haplogroups H, HV, W, K, and T. These results do not suggest continuity with local pre-Eneolithic peoples, but rather complete population replacement. We constructed maximum parsimonious networks from the data and generated population genetic statistics…We find different signatures of demographic expansion for the Tripolye people that may be caused by existing population structure or the spatiotemporal nature of ancient data. Regardless, peoples of the Tripolye Culture are more closely related to early European farmers and lack genetic continuity with Mesolithic hunter-gatherers or pre-Eneolithic groups in Ukraine.
There is stuff in the preprint about population expansion. My personal opinion is that in most cases genetics doesn’t add much beyond what archaeology does for humans in reconstructing population history. Rather, these results in concern with others are strongly indicative of population turnover. Uniparental lineages are still useful, but only in the context of other data.
The great thing about genetics when it is so clear and striking is that it clears up confusions about relationships in the past that otherwise would be unclear. It’s like having a time machine. So we now know that early European farmers (EEF) were ancestors of this particular culture. Over the next decade or so we’ll get a really granular understanding of the ebb and flow of populations across prehistoric and historic Europe. This won’t abolish all controversy, but it will reduce the space of the unknown….
I wasn’t going to do this again, but I’ve decided to promote Helix’s special discount. It ends at 2:59 AM EDT November 10th. Eight hours from when I push this post.
Obviously, there is a conflict of interest as I work for one of Helix’s partners. What does that mean?
Helix does an exome+ sequence and stores your data.
Then, you buy applications which use that data.
The company I work for is one of the application providers.
“Exome” means that Helix does a very accurate medical grade sequence of all your genes. The “+” points to the fact that they include a substantial number of positions which are not within genes (in the “junk DNA”). That totals up to 30,000,000+ markers (the exome is 1% of your whole genome). This is not trivial. Current direct-to-consumer genomics companies are looking at 500,000 to 1,000,000 markers with SNP arrays.
Helix keeps this data. Within a few months, you can buy the data at cost (it won’t be cheap!). But the model is that you buy a la cart apps, which will be affordable (our products are affordable).
I’m laying this all out very plainly because many people are asking me about these details right now as the sale winds down, and this includes people who are pretty savvy about personal genomics. Here is why I think you should get the kits now:
It gets my company more customers. That’s the self-interested part, and less important for the target audience.
For you, it gets you an exome that you can buy later without any upfront cost. For the next eight hours, Helix is basically waiving the kit costs by dropping the price $100.
Our Neanderthal product is now $9.99. Our Metabolism product is $19.99. These products are great, as they give you functional information in a very user-friendly manner. But a lot of my readers can analyze their own data, so what’s the incentive then? Again, the incentive is that you get an exome for free, and can later buy it if you want, or, perhaps even a savvy personal genomics consumer will find an app they’ll want to purchase. Normally the kit is $80, so buying it now means you’ll never have to pay this cost. If you are the type of person who has qualms about a private company keeping your data, this may not be for you.
Of course, there are other app developers in the Helix store, so just buy whatever you want. This is a way to get your exome sequenced for free now. I will tell you that the Insitome apps are among the cheapest.
Finally, a lot of people are buying “family-pack” quantities. I got four kits for example for my immediate family. Unfortunately, there are some issues with the Helix site and the extra purchases. You can buy more than one easily at Amazon right now. Our Neanderthal product is not in low stock. The Metabolism product has only a few left, though I don’t know what that means.
Note: The discount is client-side, so you may need to switch browsers if you are going to the Helix site to buy (or turn off ad-block). From what I can see Amazon does not have these issues.
Why writing up my earlier post I stumbled onto to some interesting GRE data for applicants for various countries. I transcribed the results for all nations with sample sizes greater than 500. What you see above is a plot which shows mean quantitative and verbal scores on the GRE by nations.
The correlation in this set of countries between subtests of the GRE are as so:
Quant & verbal = 0.33
Verbal & writing = 0.84
Quant & writing = 0.21
Basically, the writing score and verbal score seem to reflect the lack of English fluency in many nations.
Many of these results are not too surprising if you’ve ever seen graduate school applications in the sciences (I have). Applicants from the United States tend to have lower quantitative and higher verbal scores. This is what you see here. It’s rather unfair since the test is administered in English, and that’s the native language of the United States. No surprise the United Kingdom and Canada score high on verbal reasoning. Ireland, Australia, and New Zealand didn’t have enough test takers to make the cut, but they all do as well as the United Kingdom. Singapore has an elite group which uses English as the medium of instruction in school.
I didn’t include standard deviation information, even though it’s in there. India has a pretty high standard deviation on quantitative reasoning, at 9.1. In contrast, China only has a standard deviation of 5.2 for quantitative reasoning. More than twice as many Indians as Chinese take the GRE.
Finally, I want to observe Saudi Arabia, as opposed to Iran. Both countries have about 5,000 people taking the GRE every year. About 2.5 times as many people live in Iran as opposed to Saudi Arabia. But the results for Saudi Arabia are dismal, while Iranian students perform rather well on the quantitative portion of the GRE.* This is not surprising to me, having seen applications from Saudi and Iranian students.
Saudi Arabia wants to move beyond being purely a resource-driven economy. These sorts of results show why many people are skeptical: in the generations since the oil-boom began the Saudi state has not cultivated and matured the human capital of its population. To get a better sense, here are the scores with N’s of MENA nations and a few others:
The “natural break” is between the Saudis and everyone else. In recent years Saudis indigenized their non-essential workforce. I’m broadly skeptical of the consequences of this.
The data for the plot at the top is below the fold.
Current Anthropology has a bunch of articles related to the human settlement of Asia in its latest issue ahead of print. Aside from Martin Sikora’s most of them have a more traditional paleontological focus, so it’s pretty tough for me to understand them in context. But it’s all important to take in as we get a better and better understanding of the process.
All the articles are open access, so there’s no excuse not to read them!
One of the things that seems to be popular in biological sciences right now is the push to get rid of the GRE as part of the criteria for entrance. Two of the major rationales are that it’s expensive, so discriminates against lower socioeconomic status candidates, and, that it makes it harder to recruit underrepresented minorities since on average they score lower on the GRE (many departments have either explicit or implicit GRE cut-offs).
I’m not going to litigate these issues. To be honest I believe it is a fait accompli that many departments will stop using the GRE. This will probably increase diversity in some ways. But I also suspect it will result in a greater bias toward more “polished” candidates since very high GRE scores sometimes indicate to admissions committees that applicants who are otherwise spotty or irregular may have promise.
But, I do want to enter into the record a major problem with the argument that GRE does not correlate with academic success at the graduate level (supported by research). Yes, part of the issue may simply be range restriction. But there is another issue which many biological scientists may not be familiar with.
The standard variables considered in selecting students for graduate school do not correlate well with later measures of the success or attainments of the selected students (1, 2). The low correlations have led at least one investigator (3) to propose abandoning one of these standard variables, the Graduate Record Examination (GRE). The purpose of the present report is to demonstrate that variables that are the basis for admitting students to graduate school must have low correlations with future measures of the success of these students.
What’s going on?
As noted in the paper there are some universities which are first-choices for graduate school in a field to such an extent that they will admit candidates who have very high GPAs and very high GREs. In this case, neither of the criteria will predict success because there is very little variation to generate a correlation. But, at many universities, there is a negative correlation between admittee GRE score and undergraduate GPA. That is because very few applicants will be admitted with both low GRE and GPA scores, but some will be admitted with high GRE scores and low(er) GPAs and others with higher GPAs and low(er) GREs (usually there is still a GPA and GRE floor).
Consider the relation:
Where is the proportion of the variance of the variable you want to predict, and and are the correlations between GRE and GPA and that the variable of interest, and is the correlation between GRE and GPA.
Basically, when you have negative correlations you’re going to get into a situation where and are not going to be able to explain a lot of the variance in what you want to predict.
This may seem like a nerdy issue. And it is well known to social scientists. But since the people I see talking about the GRE are academics in the biological sciences I thought I would at least highlight this nerdy issue.
As I said above, I do think GRE is going to be dropped as a requirement at many universities for graduate programs. This is going to be a natural experiment, so we’ll be able to test many hypotheses. The paper above ends like so:
…Without a study in which a sample of the applicants-rather than of the selected students is evaluated, it is impossible to tell [the validity of the criteria -RK]. Yet such a study is completely infeasible. Even if rejected applicants are monitored throughout the rest of their working careers, it is impossible to evaluate how they would have done had they been admitted, because the rejection itself constitutes an important “treatment” difference between them and the selected students. The alternative is to admit a sample of the applicant population without using the standard admission variables to select them-preferably, to select at random.
Selection may not be random, but I believe we may be able to test some hypotheses in the next generation by testing a set of students later on after admittance on the GRE and see what the future correlation is.
Nature has an article, Pay for US postdocs varies wildly by institution. True, but as Matt Hahn, professor of biology at Indian University in Bloomington (cost of living 93% of the USA average) observed there isn’t any correction for cost of living. The researcher who dug through the data actually posted it online, so I decided to correct that oversight.
I took the institutions with N > 20, and looked up the cost of living in Best Places. The plot above is messy, but you can see that lots of institutions are paying a standard median salary of around $47,500, no matter the cost of living.
The correlation between cost of living and postdoc salary is 0.39. The weighted correlation is 0.48. These are pretty modest. That means you can find a really good situation, or a really bad one (also, institution reputation matters, there are some gems which pay well and have great reputations from what I can tell!).
Also, I’m pretty sure that the situation is worse than the numbers above suggest. Looking at the list of universities it seems there’s a bias for institutions at high cost of living locations not to want to report their salary data I think. Aside from UCSB the whole UC system denied the attempt to get data, and I don’t see Stanford, Columbia, or Harvard on the list.
The full table is below the fold, but adjusted for cost of living UCSB postdocs get $20,866 per year. In contrast, Michigan State, University of Maryland, Baltimore, and Wayne State University postdocs make more than $60,000 per year when you adjust. Stanford isn’t on the list, but online it says Stanford postdocs make between the low $50,000 to low $60,000 range, which seems reasonable for life sciences, though definitely poverty wages where the university is located (though if you are in a lucrative field it can be more, and depending on your supervisor outside consulting is a possibility, though good luck living in Silicon Valley on a $100,000 yearly gross income if you have a family, as many postdocs do).
This is pretty obvious to anyone who reads me closely. I’ve been writing and discussing with people on the internet, and in private, for many years now, and have come to the conclusion most people are decent, but they’re also craven and intellectually unserious outside of their domain specificity when they are intellectual. Many of our institutions are quite corrupt, and those which are supposedly the torchbearers of the Enlightenment, such as science, are filled with people who are also blind to their own biases or dominated by those who will plainly lie to advance their professional prospects or retain esteem from colleagues.
That’s why I laughed out loud when I saw this tweet:
A good litmus test for scientists:
What would you do if your results contradicted your political beliefs?
In psychology, much of the replication crisis was simply due to personal self-interest (more publications). But some of it was obviously political (see stereotype threat). Similarly, look at the fiasco in nutrition science. Some of it was personal, but there were also political demands from on high that there be something done. So “scholars” set some guidelines that people followed for decades, even if later they were shown to be totally ineffective. I’m not even going to get into the travesty that is modern biomedical science, with professional advancement and institutional interests combined in a deadly cocktail.
Also, I enjoy science popularizing (or did, I don’t read science books much anymore) as much as the next person, but isn’t it interesting how much of modern science confirms the mainstream elite cultural norms of ~2020? Curiously, if you read science popularizations in newspapers in 1920 they would also confirm the elite cultural norms of 1920…. But this time we’re right!
Other institutions aren’t doing better. The media is going through economic collapse, and journalists and their paymasters are reacting by pandering to their audiences. Instead of illuminating, they’re confirming. That’s what the audience wants, and I’m sure it’s more satisfying to journalists anyway. But can you blame them with the economics that are before us?
Don’t get me started on Facebook or Twitter.
I was having a discussion with a reasonably prominent pundit (you would recognize the name) today who bemoaned the reality that so many journalists are now driven to sating tribal passions and generating clicks for their paymasters. He was trying to argue against my pessimism, suggesting that the fever was starting to break. We’ll see. I hope I’m wrong.
People have always been biased and subject to motivated reasoning. We’ve had our disputes whatever our ideology, whether it be conservative, moderate, or liberal. But the Enlightenment perspective of critical rationalism, which took philosophical realism seriously, meant that ultimately people who disagreed often assumed that fundamentally they were trying to converge on the same facts, the same reality. Reality existed, and you couldn’t just wish it away. Discussion might forward two individuals to a convergence!
We’re not there anymore. Whether it be Bush-era contempt for “Reality-Based Community”, or the rising crest of “Critical Theory”, the acid of subjectivism is eroding the vast edifice of aspirational realism which grew organically in the wake of the Enlightenment. This isn’t a Left vs. Right phenomenon, it’s a human dynamic, because for most of human history what is true has been determined by what the tribe dictates to be true, and what the tribe dictates to be true has often not been based on a critical evaluation of facts and theories. What the tribe dictates to be true is computationally less intensive than thinking things through yourself, and, it’s often right-enough.
The reality is that this cultural cognition and conformity has always held. It’s just that it seems that for a few centuries substantial latitude was given in public to a relative amount of heterodoxy from broad tribal visions. And it was always a work in progress. But there was a goal, and an ideal, even if we habitually failed. We failed in the direction of truth.
We live in a post-modern age now. Feelings are paramount, facts must bow before them. But the curious fact is that the post-modern age is just the pre-modern age. When I first read the Christian author Alister McGrath I literally scoffed at his contention that atheism would fail before the ascendancy of post-modernism. Ten years on I will admit that I now believe he was right and I was wrong. Though I don’t think the New Atheism failed miserably, I do think that the problems it is encountering from the cultural Left are due to its cold modernist baggage.
No truth, no liberalism. No liberalism, and democracy become the mob. The passions of the mob do eventually fail, and its wake a more oligarchic and hierarchical system will emerge. We may simply be seeing the end of the liberal individualist interregnum, as history reverts to its despotic collectivist norm.
Art, the applied sciences of engineering, and many human endeavors will continue to develop in the new order. Illiberal societies, all societies until recently, can be cultured and civilized. My own preference is for the dignity of the individual and legal egalitarianism of the liberal world in which I grew up (but in which I was not born), but humans have flourished and continue to flourish in illiberal environments.
One way to think about the past century or so is that more or less the waters of human nature receded, and a great undersea world was exposed. But now human nature is rising, and that world is submerging before our eyes. But islands of the old world we grew up in will persist. We need to find each other out and cherish the values of critical inquiry as we have for thousands of years. An archipelago of learning for learning’s sake can sill maintain itself in a world where our values no longer hold the leash. But like the mammals during the Mesozoic, we will have to go back into the night and the shadows. There will hopefully be oligarchic patrons who sympathize with us, and despots like Frederick the Great who give us some latitude to work. Our values will fade and diminish, but they will not disappear.* One day they may come to the fore again!
Finally, understanding that most people don’t need to be right or utter the truth, but simply need to win, has made me much more cheerful and less sour observing everyday stupidities. It is no great insight to observe that I’ve never been one who has had much esteem for the admiration of my peers. I like to do my own thing. But tribal acclamation must be the best of all things for most humans, and now I understand why they fight unfairly and stupidly with such ease and naturalness: their aim not to be right in the eyes of nature, but to rise in the esteem their fellow human. That is the summum bonum.
Note: I’ll be very happy to be proven wrong in 15 years. But as it is I think by then we’ll be dealing with the final breakdown of the institutions of the republic in the wake of a Left-wing attempt to forestall the economic immiseration of the middle-class that failed.
* The main reason I hated religion as a child is the mindless boredom of attendance at services. I quickly realized I didn’t believe any of that tripe and never had. But the liberty that I have to dissent from public values may not be a liberty we always have. Private dissent may come back and become the norm as it has been for much of human history.
Will try to keep self-interested product placement to a minimum normally, but I thought I’d pass on that Helix has a $100 off sale for the next 72 hours. That means that the company I work for has a Neanderthal app on sale for $9.99. The regular price is $29.99, and added $80.00 for exome+ sequencing if you aren’t in the Helix database (which most people are not).
The upshot here is that the $9.99 will get you an exome+ sequence, which at some point in early 2018 you can download for $600. But if you don’t want to download it it’s a great way to get into the ecosystem on-the-cheap.
I assume most of my readers know what the exome is, but it’s basically the portion of your genome which is directly translated into functional proteins. That’s about ~1% of the genome, or ~30,000,000 bases. This is a major expansion on the SNP-chip platforms which are DTC which are in the 500,000 to 1,000,000 SNP range.
Anyway, not sure this will be appealing to readers who need a full download of data. But if you are the type who is more interested in getting applications related to your genome, this is a pretty good deal at a sub-$10 price point.
Note: To my knowledge only ships to USA currently.