Well, well, well…look what just got published in Nature

Nature‘s Journal of Human Genetics, that is. It’s a little piece titled “The collective effects of genetic variants and complex traits” by Mingrui Wang & Shi Huang, and the abstract is a bit odd.

Traditional approaches in studying the genetics of complex traits have focused on identifying specific genetic variants. However, the collective effects of variants have remained largely unexplored. Here, we evaluated whether traits could be influenced by the collective effects of variants across the entire protein coding-region of the genome or the entire genome. We studied the UK Biobank exome sequencing data of 167,246 individuals as well as the genome-wide SNP array data of 408,868 individuals. We calculated for each individual four different measures of genetic variation such as heterozygosity and number of variants and two different measures of the overall deleteriousness of all variants, and performed correlations with 17 representative traits that have been studied previously. Linear regression analysis was performed with adjustment for age, sex, and genetic principal components. The results showed a high correlation among the six different measures and an inverse association of two well-correlated traits (educational attainment and height) with the total number of all variants as well as the overall deleteriousness of all variants. We have also categorized the genes based on whether they are expressed in the brain and found that the association with educational attainment only held for the brain-expressed genes. No other traits examined showed a significant correlation with the brain-expressed genes. The study demonstrates that common traits could be studied by analyzing the overall genetic variation and suggests that educational attainment is inversely related to genetic variation.

Basically, the authors did some correlations on genomic data in a database, and they think they’ve found an inverse association — high genetic diversity in a population is coupled with low educational attainment. That is, coming from a region with high genetic diversity, like say, Africa, is correlated with, for instance, lower education. To which I would suggest that maybe that’s not surprising, that a continent that has been exploited and colonized for centuries, might have historical reasons for its people not having the advantages of the colonizer countries. But this paper wants to imply that that educational handicap is genetic.

Who reviewed this thing, anyway?

The authors use cautious wording in the abstract. The corresponding author, Shi Huang, is letting his racist freak flag fly on Twitter, though. He’s explaining how we’re supposed to interpret it.

Our latest paper. We show that genetic diversity is a new genetic factor in cognition, challenging the Out of Africa model. GD in human is under selection and has little to do with long evolutionary time or being human ancestors.

Excuse me? We’ve already gone from “educational attainment” to “cognition,” which is enough of a leap, but he’s somehow using these correlations to claim that modern humans did not evolve from African ancestors? Data not shown. Then, remarkably, he claims that genetic diversity is somehow selected for, that it has nothing to do with history or ancestry. Fucking data not fucking shown. This makes no sense. How does he get to this conclusion?

The San have the highest GD and the lowest cognition/civilization in humans and are believed to be the ancestors, i.e., Out of Africa. The only alternative is the maximum GD theory that GD has an upper limit, which is inversely proportional to brain function or complexity.

That this African group have high genetic diversity compared to other populations has been noted before, but “lowest cognition”? That’s absurd. This smacks of the discredited pseudo-scientific racism of Shockley and Lynn. “Lowest civilization”…again, how do you measure that? It’s more Western bias.

Then he completely demolishes his credibility. No one believes the San are the ancestors of other groups of people; they can’t be. They’re a modern human culture. They’re as derived as any other population on the planet, equally divergent from our shared distant ancestors. This guy is a professor of genetics? And there he goes again, blithely transforming “educational attainment” into “brain function or complexity.” That’s not valid.

The thread just goes haring after all kinds of absurdities.

This inverse relationship holds well among species (the higher the complexity, the lower the GD), which means that the highest GD of the San may be the reason for their cognition level being the lowest. The origin of humans may actually not be in Africa but in E Asia.

Wait wait wait. So he’s arguing that highly inbred species with high degrees of homozygosity, like many lab animals, are going to have a higher “cognition level” than wild and genetically diverse animals? How did he measure “complexity”? He’s claiming a correlation throughout the animal kingdom, did he really measure the genetic diversity of a large number of species and show that small-brained species are a causal consequence of having greater genetic diversity? Alternative hypothesis: the larger your brain, the more specialized in that category you have to be, and the smaller your population size can be, thereby limiting the number of variants that can exist in the population. You aren’t large-brained because your population has limited diversity, and also, because all Shi Huang has done here is a correlational analysis, he can’t claim causality.

He really has a bug up his butt about the out-of-Africa model. I suspect it’s more about not wanting to have African ancestors, and is fundamentally a racist bias.

For completeness’ sake, here are the rest of his claims. I don’t care anymore. He’s a fool.

Our study analyzed genotype/phenotype from more >400,000 people in the UK, calculated multiple measures of GD for each individual, and examined which traits these measures were associated with using linear regression analysis that has controlled for confounding factors.
Among 17 traits examined, only education attainment, a proxy of IQ, has the best association (inverse) with GD. Only brain-expressed genes, but not brain-non-expressed, showed an association. The association of non-syn variants is higher than that of syn or intronic variants.
Low cognition is subject to natural selection, and so the underlying GD must be also rather than being time-related and not subject to natural selection as assumed by the molecular clock and neutral theory. The finding challenges the assumption of the OOA model.

I tried to dig deeper into who this guy is, but was repelled because he seems to be beloved by the scientific racists. For instance, I got a little of his background from the Free Times (FriaTider), a radical right wing newspaper in Sweden.

Shi Huang received his doctorate from the Univ. of California… and then worked… for a couple of decades, including as an associate professor at The Sanford-Burnham Institute. In 2009 he moved back to China and has since been a professor at Central South University in Hunan. Today he has a professorship in genetics, epigenetics and evolution…

Unfortunately, I got there from a horrible racist blog called “subspecieist”, which, I’m sorry to say, I won’t link to because it is so deeply despicable, but I will mention a previous “discovery” by Shi Huang that got them extremely excited.

Geneticist Dr. Shi Huang: Shocking evidence, Africans closer genetically to Chimpanzees than Eurasians

Jesus. What an ignorant crock of shit. No. That makes no sense at all. Both modern Africans and modern Eurasians are equally distantly removed from our chimpanzee ancestors. Shi Huang really desperately wants to argue that he didn’t have any black ancestors, I guess, and he’ll make all kinds of illogical leaps to demonstrate that.

And this crank still gets published by Nature.

The crisis of gullibility

Follow the dogwhistles

I feel like I’ve been railing against nonsense for my entire life. I got into the skepticism side of everything starting with my opposition to creationism — there I was, diligently studying developmental and evolutionary biology, and I started encountering these raving loons who outright rejected all of science while claiming the earth was 6,000 years old and that all life was magically created in a short week. It was offensive. It was absurd. Yet those kooks continue to thrive.

Since then, the bullshit has continued to pile up. We have flat-earthers, anti-vaxxers, QAnon conspiracy theorists, sovereign citizens, crypto fanatics, and satanic panics, all patently bogus, and they have led to a world of transphobia, homophobia, insurrections, armed militias, anti-education sentiment, and a Supreme Court and Congress packed with some of the dumbest idjits ever to grace this country. People hold the incredible as credible. The media take the silly seriously.

What is going on? It’s an epidemic of idiocy.

I admit that I live in a bubble of sanity, but people outside that bubble aren’t stupid. They’ve been misled and misinformed, their fears have been stoked, but the people wearing MAGA hats and attending anti-vax rallies are also a minority. Perhaps a growing minority, but still…they shouldn’t have as much influence as they do. In a sensible world, they ought to be laughed at.

I’m going to blame social media. I saw it on Facebook, with old friends getting sucked down into a vortex of insanity, people self-reinforcing each other over the latest extreme conspiracy theory, which would be actively promoted by the medium. It was an environment designed for kooks; they got free license to say anything, which was fine, but then criticism of bad ideas was walled off and contained, so the circle-jerks grew unchecked. If you dared to speak up and say, “Errm, the world is round, all the evidence says so” you would be shouted down by a massive crowd of people finding confidence in their numbers. It was ugly. I finally had enough and had to leave that site, cutting off all connections and closing my account.

Now it’s Twitter. This service has the potential to be even worse than Facebook, because now it has been bought up by a billionaire with bad taste and bad ideas who is endorsing QAnon, going full anti-vax, and calling for Fauci to be imprisoned. He’s insane. He’s going to lead Twitter into full collapse as a madhouse of raging nitwits.

That also leads into another big American difficulty — the way unfettered capitalism has produced a class of overvalued morons who can buy further degradation of the system.

It’s a nightmare, and I can’t abide it. I’m eventually going to have to kill my Twitter account, in the same way I murdered my Facebook account. Right now, I’m using Twitter as a free advertising service for the blog, and that’s it. I post links to Pharyngula there, but I am as of this moment refusing to engage further on the site: no other chatter, no conversation, no discussion — if you want to talk to me (and I do want to talk with other people), we’ll all have to make the effort to find other ways to engage. I’m on Mastodon, I have YouTube, and most of all, I have Freethoughtblogs.

I don’t know what else to do. Social media is a failed experiment that has had disastrous consequences. Bring back RSS!

Greetings from my new world

It’s all different now. Yesterday was the day of my last big effort in the fall semester, when I sat down for most of the day to put together two final exams. I got them done! I posted them online! The ball is in your court now, students! My sense of relief was immense. It was so great that I went online and watched a movie*, while not feeling the customary dread that I’d forgotten something.

I’m not quite done, but it’s just clean-up left. I have an administrative meeting this morning, and I’ll have to grade those finals this weekend — but one is an optional exam that only a few students will take, and the other is designed to be machine-gradeable.

This morning I woke up to incredible silence. We’re at the beginning of a major snowstorm, and everyone is staying home, swaddled up to keep warm. No cars! Everything is blanketed with snow, muffling the sounds further! Even the birds have gone silent! It’s a good thing my exams are all totally online, everyone should stay safe at home. It’s still snowing, and is expected to snow all day, and keep snowing through Friday.

I should probably stay home too, but I might get out for a walk this afternoon, if it isn’t too icy. Big fat flakes coming down, temperatures that are reasonably warm (right around 0°C), that’s pleasant.

Man, it feels good to shed that load that’s been clinging to my back the last few months.

*The movie was Slash/Back, an Inuit/Canadian horror movie. I liked it! The setting gave a glimpse into the lives of a group of Inuit kids — there were honest illustrations of poverty and alcoholism, but also showed off their amazing self-reliance and casual adaptability. The alien monsters were cool and creepy, too. On the negative side, these kids were clumsy self-conscious actors, the ending was a bit abrupt and rather pat, but I forgave it all for being refreshingly different. I enjoyed it more than the last slickly-made Marvel movie I watched.

SBF is finding out

Every where I turn, there’s another interview with Sam Bankman-Fried. He’s been chattering away like a chimpanzee on meth to anyone who asks for a few minutes of his time.

Bankman-Fried has spent the past few weeks in his Bahamas estate, giving numerous interviews to reporters and making dozens of social media posts trying to explain how his company went from being one of the biggest and most-respected crypto exchanges to filing for bankruptcy after it could not meet its customers’ withdrawal requests. The company owes its top creditors $3 billion, according to bankruptcy filings, and investigators have sought answers on whether it used customer funds to lend money to Bankman-Fried’s investment arm, Alameda Research.

Bankman-Fried has said he made grave mistakes but has denied any malicious wrongdoing.

Yeah, “mistakes”. Is that what we call gross negligence, incompetence, and profiteering? Sure. “Mistakes.”

All those “mistakes” are adding up to this result:

Sam Bankman-Fried, the founder of the collapsed cryptocurrency exchange FTX, was arrested Monday in the Bahamas after U.S. prosecutors filed an indictment against him.

Good.

I felt a little twinge of the Christmas spirit

It was tiny, mind you, but for just a moment I felt a little holiday joy.

You all know who Dave Chappelle is — once a ground-breaking comedian, now a cranky, transphobic, anti-woke whiner. He still gets comedy concert gigs, but you know his audience has shrunk to just the kind of people who don’t mind a bitter, cruel joke about trans people. He put on a show in San Francisco, which is still his kind of place, a venue where he could pack in the tech bros who usually aren’t very socially conscious, and he brought on stage…Elon Musk. I followed this online, expecting in my grinchy, cynical way, that this was the crowd that would applaud a transphobe and a greedy bumbling billionaire.

That I simply MUST hear!
So I paused.
And the Grinch put his hand to his ear.
And I did hear a sound rising over the snow.
It started in low.
Then it started to grow…
But the sound wasn’t cheery!
Why, this sound sounded angry!
It couldn’t be so!

They despised him! They hated him! They booed that motherfucker for ten minutes straight!

Then the Grinch thought of something he hadn’t before!
Maybe Christmas,
I thought
doesn’t come from a store. Maybe Christmas…perhaps…means a little bit more!
And what happened then…?
Well…in Who-ville they say that the Grinch’s small heart Grew three sizes that day!

Well, maybe a size and a half. I’m not that easy.

The icing on the cake was seeing Chappelle stoop to defend Musk by insulting his audience. They must be poor! They must be the people he fired!

All these people who are booing, and I’m just pointing out the obvious, you have terrible seats.

That’s Dave for you, the once great comedian, reduced to mocking people for being poor, as he panders to the richest man in the world.

Good night, Elon. You’ve fallen and won’t be getting up again.

“Get a job,” they say, and wonder where the artists went

Research in the UK reveals a decline in the proportion of people employed in creative work. That’s not good.

The proportion of working-class actors, musicians and writers has shrunk by half since the 1970s, new research shows.

Analysis of Office for National Statistics data found that 16.4% of creative workers born between 1953 and 1962 had a working-class background, but that had fallen to just 7.9% for those born four decades later.

I wonder why. The article doesn’t get around to giving a good explanation; there’s one waffling attempt to wave it away by saying that there is a smaller pool of working class people to draw from now, as if everyone is just wealthier now so naturally you’re going to have fewer lower middle class people going into the arts. But then, I’m confused by what they also say:

The finding raises questions about why years of attempts to make the arts more open and diverse have not had more impact – people who grew up in professional families were four times more likely than those with working-class parents to be in creative work, the study found.

But then, if everyone is generally moving up to the professional class, shouldn’t there be a flowering of the arts in the UK? I don’t think we’re getting the full story here. I’d want to know the change in proportion of creatives from the whole population, not just a single class. It makes the story uninterpretable to leave that out.

I would suggest though, that from the American side, part of the story has to be the transformation of education from an endeavor to help people learn more to one that’s all about landing a good job. And that change is driven by the fact that higher ed has become so expensive that it’s pricing itself out of reach of the working class. Even in the 1970s, as a member of a working class family, college was not encouraged — in those years, I could pay for it with part-time and summer work, but it meant delaying getting a good union job in a trade for four years, and that was lost income. Now you go to college, it means racking up $100,000 in debt. You better not major in poetry or literature or dance with that kind of debt hanging over your head! Computers and chemical engineering, on the other hand…