Bad genetics exposed

If you read Nathaniel Comfort’s scathing review of Robert Plomin’s book, Blueprint, you ain’t seen nothin’ yet. He was holding back, maintaining the decorum of the journal as best he could. He gives a more thorough criticism on his blog, Genotopia, and wow, it’s even more brutal. Sometimes a more thorough and nuanced analysis just leads to an even stronger condemnation.

…Plomin’s argument is socially dangerous. Sure, genes influence and shape complex behavior, but we have almost no idea how. At this point in time (late 2018), it’s the genetic contributions to complex behavior that are mostly random and unsystematic. Polygenic scores may suggest regions of the genome in which one might find causal genes, but we already know that the contribution of any one gene to complex behavior is minute. Thousands of genes are involved in personality traits and intelligence—and many of the same polymorphisms pop up in every polygenic study of complex behavior. Even if the polygenic scores were causal, it remains very much up in the air whether looking at the genes for complex behavior will ever really tell us very much about those behaviors.

In contrast—and contra Plomin—we have very good ideas about how environments shape behaviors. Taking educational attainment as an example (it’s a favorite of the PGS crowd—a proxy for IQ, whose reputation has become pretty tarnished in recent years), we know that kids do better in school when they have eaten breakfast. We know they do better if they aren’t abused. We know they do better when they have enriched environments, at home and in school.

We also know that DNA doesn’t act alone. Plomin neglects all post-transcriptional modification, epigenetics, microbiomics, and systems biology—sciences that show without a doubt that you can’t draw a straight line from genes to behavior. The more complex the trait in question, the more true that sentence becomes. And Plomin is talking about the most complex traits there are: human personality and intelligence.

Plomin’s argument is dangerous because it minimizes those absolutely robust findings. If you follow his advice, you go along with the Republicans and continue slowly strangling public education and vote for that euphemism for separate-but-equal education, “school choice.” You axe Head Start. You eliminate food stamps and school lunch programs. You go along with eliminating affirmative action programs, which are designed to remediate past social neglect; in other words, you vote to restore neglect of the under-privileged. Those kids with genetic gumption will rise out of their circumstances one way or another…like Clarence Thomas and Ben Carson or something, I guess. As for the rest, fuck ’em.

I can see how that wouldn’t get printed in Nature, but he’s exactly right on every single point. Plomin, no matter what his own political views, has written a garbage book that plays right into the hands of the right wing, from the title onwards. It’s shocking that Plomin is completely oblivious to how crude and wrong his understanding of modern genetics is…a lock of understanding that allowed him to write a whole book on his ignorance. It’s a bit like Nicholas Wade’s book, A Troublesome Inheritance — another instance of Dunning-Krueger fused with 19th century racism.

Hey, though, if you care about this stuff, and are interested in how good science can be communicated well, I have a treat for you: tomorrow, Tuesday, at 6:30 Eastern, you can tune in to an online discussion between Jennifer Raff and Carl Zimmer on Why You’re You: Explaining Heredity to a Confused Public.

Note that this is not a debate — it’s a conversation between two well-informed individuals on good science, and how to explain it. I’ll be checking in!

This is an age of thuggery

It’s Monday. Get depressed even more. Read David Neiwert’s summary of right-wing extremism. A few excerpts:

And now we have gangs of heavily armed right-wing thugs, largely outsiders from rural and exurban areas, invading liberal urban centers with the full intent of provoking violence so that they can portray the American left as innately violent.

I’ve covered about a dozen of these events. I hang out among the alt-righters and militiamen who populate that side and listen to them. They all are brimming with eagerness to beat the shit out of liberals, and they’re prepared to kill if they deem it necessary.

The Proud Boys are selling t-shirts that celebrate the idea of throwing liberals out of helicopters, emulating the Pinochet regime. That’s right. They’re openly promoting the idea of “Right Wing Death Squads”, and they think this would be a great thing.

So now the faction that has long fantasized about civil wars is openly fantasizing about murdering their fellow Americans by various means, most of them as cruel as a good psychopath can dream up. These folks are fanatical authoritarians.

And they are entirely right-wing. There is no counterpart to this on the left. Even the most rabid anarchist/communist/whatever group doesn’t direct this kind of rhetoric at its opponents. Moreover, the far left is a tiny and powerless faction. Unlike the alt-right.

Moreover, it is the far right that now controls all three houses of government in the United States. And the most powerful of all, the president, has a long habit of using eliminationist rhetoric to attack his opponents: “Lock Her Up!” was just one of many such.

Now he is describing half of America – the larger half that did not vote for him, and which now opposes his agenda at every turn – in such terms. Dismissing them as a “mob” and suggesting that they not only cannot govern but cannot BE governed is lethally dangerous.

Yet to hear the centrist media figures and their favorite subjects, centrist politicians, discuss all this ferment, you would think that both sides are engaging in this kind of prewar rhetoric. It’s absurd.

So, listen up, Chuck Todd, Evan McMullin, Susan Collins, and every other hand-wringing centrist wannabe: IT’S NOT BOTH SIDES. Only one side is trying to gin up a civil war in this country.

But it’s not just the USA. Look at Brazil, where elections may make Jair Bolsonaro, AKA “the thing”, president. A few quotes:

• “I had four sons, but then I had a moment of weakness, and the fifth was a girl.”

• “I’m not going to rape you, because you’re very ugly” – to a female representative in Congress.
[That one echoes Carl Benjamin, AKA Sargon of Akkad, who insists that phrase is not a threat. Good work, Carl, sharing slogans with a monstrous thing]

• “I’d rather have my son die in a car accident than have him show up dating some guy.”

• “I’m pro-torture, and the people are too.”

• “They don’t do anything. I don’t think they’re even good for procreation any more” – referring to quilombolas, the black descendants of rebel African slaves.

His followers also have a charming t-shirt to advertise their position: it features the face of “one of the most sadistic torturers and murderers in the military dictatorship that choked Brazil between 1964 and 1985”. How can such a thug become a leading contender for the presidency? I think we Americans can guess: by forming a coalition of religious bigots, the obscenely wealthy, and racists, and because the opposition party is ineffective, unfocused, and uninspiring.

In the cities, he has the support of the leaders of evangelical religious empires, who defend the concept that marriage is possible only between a man and a woman. The far-right candidate also leads among wealthier, more educated men, reflecting the calibre of the Brazilian elites.

In addition to his staunch supporters, he attracts a slice of the population that is simply anti-PT [PT=the Workers Party]. These people hate the PT for many reasons. Some because under former presidents Luiz Inácio Lula da Silva and Rousseff, the party reduced poverty, widened university access to black students, and strengthened rights for housemaids – for a long time, a form of modern slavery in Brazil. Others because they cannot forgive a party that rose to power promising change, only to become corrupted and aloof. Poor, mostly black, women are most vociferously against Bolsonaro.

Jebus, that sounds painfully familiar. Even the part about black women being the most reliable leaders against misogyny and racism.

Now if only there were a way to form a coalition of humanists, egalitarians, scientists, decent people from all walks of life, who didn’t brag about compelling authority at the point of a gun, didn’t celebrate torture and murder in their slogans, and didn’t live to serve the whims of the extremely rich, maybe we could make some headway against the forces of thuggery. Somehow, a t-shirt that announces “We won’t throw our fellow citizens out of a helicopter!” just isn’t very compelling, maybe because it’s declaring something that we ought to take for granted, and find hard to believe that anyone would disagree. If you’re one of those “hand-wringing centrists”, anyway, you’re fine with sitting in your safe, quiet lair surrounded by people exactly like you, who aren’t threatening you, because they’re busy threatening other people.

Susan Collins can smugly dismiss those others, because the Republicans are sucking up to her — while her colleague Orrin Hatch can sneer at victims of sexual assault, and her president can mock them at rallies. Meanwhile, Christine Blasey Ford is still in hiding and still receiving death threats.

But oh no, there are decent people on both sides.

And that’s how the Republic will fall — because we lie to ourselves about the severity of the threat, refuse to believe that murderous thugs even exist, and roll over and let them seize power, enabled by these contemptible apologists.

John Oliver has a few things to say about the Brazilian election.

ACCUSED MEN ARE THE VICTIMS HERE

Lawrence Krauss is in big trouble at ASU.

A college dean has recommended prominent theoretical physicist Lawrence Krauss, who was accused of sexual harassment, be fired from Arizona State University.

Whoa. That’s a major threat to his academic career. It’s too bad he is totally helpless before the accusations of women, and has no defense against this witch hunt.

Oh, wait…

According to policies set by the Arizona Board of Regents, Krauss is entitled to several layers of review before he can be fired.

First, the dean of a professor’s school can recommend a faculty member be dismissed, which is what Kenney did. Then, the faculty member can challenge the recommendation in what is called a conciliation or mediation, and a conciliation committee comprised of faculty members is set up.

Krauss is in the conciliation process right now, a university spokesman said. Kenney, Krauss and the president of the University Senate all appointed one member to serve on the committee.

The conciliation committee’s goal is to find a “mutually agreed upon solution,” according to Board of Regents’ policy.

If the conciliation process fails, Crow can issue a written notice of dismissal. Krauss could then appeal this notice to the Committee on Academic Freedom and Tenure and receive a hearing.

The committee makes a recommendation to Crow, who then makes a decision on dismissal. Krauss has another opportunity to ask for reconsideration before a final decision from Crow.

The entire process can take many months.

Not to mention he is on a fully paid leave. I’m also on leave from my university, but if you take a sabbatical for career development, they reward you with half pay. If only I’d been fondling women, I could be getting full pay! The mistakes we make…

Also not mentioned is that, as a popular physics superstar, he’s got his book revenues to fall back on.

I’m also going to give him 6 months if he loses tenure (not a sure thing at all) to be back on the comeback trail, getting more speaking gigs, another book deal, maybe a position at another university, because after all, hasn’t he suffered enough?

(I’ve just learned that this much sarcasm hurts my heart. Need to stop doing that.)

Planned Parenthood is here for good

While we were driving to Minneapolis, we had to pass through Jebus Alley, the corridor that runs through the middle of the state, and which is festooned with billboards from obnoxious evangelical churches and Pro-Life Across America. I usually just snarl and move on. But this time — I saw an amazing sight. I saw…this:

It’s about time. IN YOUR FACE, YAHOOS.

Sure looks like design to me!

I attended a lecture by Dave and Mary Jo Nutting of the Alpha-Omega Institute, a creationist…well, I was going to say “think tank”, but it’s really just an apartment in a building that also houses a cleaning service, and is nothing but Dave & Mary Jo promoting themselves as speakers, and there isn’t much thinking going on. What is it with creationists putting pretentious labels on their homes?

Which reminds me…I’ve got to get that sign for the “Institute of Eight Legged Freaks, Departments of Mollusca and Arachnida, and the Academy of Pharyngula Studies” made up for my lawn.

Anyway, it was terrible. Godawful boring and repetitive. Two and a half hours long. Fucking dreadful, even for the low expectations I have for creationists. I sat through the whole thing, seething, until I erupted a little bit in the Q&A.

My wife doesn’t go to these things, but this time Mary came along. I think she wanted to make sure I didn’t misbehave. She doesn’t like to make a scene, so when I started chewing out these ignorant frauds, she was right next to me, drilling her elbow into my ribs. It was a bit uncomfortable, but I persevered. But ow, my side aches today.

Anyway, you probably don’t want to listen to the whole thing, even though I recorded it all. I can summarize it for you: Dave briefly shows an example of a scientific discovery, like the blood clotting pathway, or dolphin countercurrent exchange systems, or DNA repair mechanisms, and then announces, Sure looks like design to me! Over and over. He doesn’t actually address any of the mechanisms behind any of the phenomena, or discuss the evidence, or fairly present the evidence for their evolution — he relies entirely on the pretense that complexity and/or function are synonyms for design. So he throws up an abridged slide of the clotting pathway, and then slaps a label on it claiming it’s all evidence for creation.

It was a poorly attended talk, and I can understand why — they were utterly inane. The Q&A got a little more interesting, largely because every question was pushing back against their claims. If there were attendees who were pro-creationism, they were utterly silent the whole long evening.

At the end, in the Q&A, I rudely called bullshit on them. Look: complexity and functionality are outcomes of a process. We all agree that biological systems are functional and often complex. The question is about the nature of the process. Biologists say there are natural mechanisms that can generate those outcomes, and we have bucket loads of empirical evidence that allow us to explain how functionality and complexity are generated, to widely varying degrees of thoroughness. Creationists say there is one explanation, an explicit act of intentional creation by a designer, and have no evidence whatsoever for it, other than a Gomer Pyle-like expression of incredulity that revels in their ignorance of what the scientists have said.

When I pointed out this disconnect between evidence and their conclusion, and that they are falsely equating complexity with intentional design, Mary Jo denied it. Then she said it wasn’t just complexity, but the intricacy and interconnectedness of organization, which is just throwing out some new nouns and adjectives that say exactly the same thing: complexity equals design. They really have no idea about what they’re talking about.

This was demonstrated perfectly in the first question, at about 1:40. What is it exactly about finding a watch on the beach that tells you it is designed? The reply: I see organizational structure. I see function. A follow-up question was roughly, “if everything is designed, how would you recognize something that wasn’t designed?” To which they said there is also some randomness, giving them an excuse to babble about a tornado in a junkyard assembling an airplane.

The second questioner asks for a clarification: that they’re talking about these crazy complex systems to show that chance is insufficient to explain them. I believe things are too complex, so there must have been a designer. Then he asks about the possibility that design is simply an interpretation based on human bias and experience. They don’t seem to understand the point: Mary Jo goes on about how a building must have a builder. Dave’s answer is familiar: Based on what we see and know, it sure looks designed. Then he goes on to say it taxes credulity to think it could have happened by accident. Wooooooosh, way over his head.

The third question asks whether they understand the argument from ignorance, or the argument from personal incredulity. Nope. They had to ask him to explain it. In a follow-up, he points out that he can’t see the difference between their argument, and saying a magic pixie did it. Mary Jo counters by saying that they have to use other evidence, like historical evidence…by which she means the Bible.

She keeps talking. The talk was long-winded, their answers were equally long-winded. She starts off with the complexity thing again, saying that molecules bouncing around randomly can’t explain complexity.

That’s where I finally erupt and tell them they can’t do that — it’s an invalid argument to simply claim complexity is sufficent to justify the design explanation. (Warning: I come off very loud, like the voice of God, but it’s only because my recorder was sitting on the desk directly in front of me). She replies by saying it’s not just the complexity, it’s the ordered complexity. Jesus fuck, they are dense. Systems, machines, computers. Mindless buzzwords.

Another question: what about species that go extinct? Guess what the answer is?

Yeah, The Fall. The Flood.

A follow-up: Given the Flood, how did organisms repopulate the earth? Perhaps they hopped.

There was another question about biogeography after the flood. I felt like shouting, stop pandering to their delusions. There was no flood. It just gives them opportunity to meander on with Bible stories.

Next question: Why do you prioritize supernatural answers over natural ones, when we’ve never seen anything propely answered with supernatural explanations? The supernatural makes more sense to us. Also, an admission: we have no evidence.

Next: questioner brings up an example Nutting used, of a sea slug that eats anemones and recycles nematocysts for their own use. Did that happen before or after the Fall? They don’t know.

It came around to me again. I demanded that they show evidence for design other than reiterating the mantra of complexity. Their argument, after I told them that just claiming evolution relies only on chance is dishonest, was to argue that natural selection can only act on what is already there. I mentioned biology as a property of chemistry; they claimed that chemistry is evolution. What I didn’t bring up, and should have, is that they’ve just pushed back their unanswerable questions of evolution to prebiotic chemistry, which doesn’t fit with their claims of a 6000 year old earth and a global flood.

The next question is a conciliatory comment in which the questioner says he appreciates the sincerity of their beliefs. But then he asks a really good question. He asks how they explain that their position is becoming less popular. And that’s true: there might have been 20 people in the audience, and judging by the questions, almost all of them completely disagreed with the Nuttings.

Their answer is that all that’s taught at the university is naturalism. They also blame separation of church and state. You’ve been brainwashed, sheeple!

Next question: The Nuttings believe as they do because of personal experiences; the questioner accept the concensus of science. Do they believe personal experience over empirical evidence? They waffle pointlessly. They don’t reject empirical evidence (which wasn’t the question) they just…I don’t know what. So the question gets repeated. There’s way too much that indicates there must be a designer. Then he starts babbling about the Bible.

I count that as a total non-answer.

Next: it’s pointed out that science doesn’t work the way they claim. It’s not a collection of facts followed by interpretation, where every interpretation is equal. Science builds on progressive hypothesis testing; they put up slides of the end conclusions of a lot of work to giggle over, but that was all based on a lot of legitimate work that they didn’t show. Mary Jo offers vague agreement that there is a process of science, but claims it doesn’t tell us how it got there. I’d say it does; they just intentionally neglected to discuss it. In follow up, the questioner points out that invoking the supernatural basically kills our ability to address the question, and returns to the initial question of how you recognize undesigned organization. It’s mentioned that the hypothesis that the devil buried all those fossils is a supernatural explanation. The moderator says that their organization (Maranatha) doesn’t believe that — which misses the whole point. How do they know?

The next question hammers on a point that had been made a few times: biology doesn’t explain the world in terms of pure chance. So why do the Nuttings keep going back to this claim of nothing but random chance? Dave replies by asking, rhetorically, if he thinks protein folding is purely chemistry and natural laws. He then claims that natural laws…are not going to do that. It’s a folding machine. (Throughout the evening, “machine” was their magical word to imply a process was artificial.)

I will also remind you all that the title of the talk asserted a dichotomy, Grand Design vs Chance. This was a fundamental issue, and they didn’t address it.

And with that, I’d had enough. We left.

You can listen to the whole thing, if I haven’t sufficiently discouraged you.

Not incivil enough

Chuck Wendig eloquently says what I think.

There will be renewed calls for civility. Ignore them. They ask for civility as a way for you to grant them complicity in what they do.

Civility is for normalcy. When things are normal and working as intended, civility is part of maintaining balance. But when that balance is gone, civility does not help return it but rather, destabilize it further. Because your civility gives them cover for evil.

Note: this isn’t the same as calling for violence. But it is suggesting that you should not be shamed for using vigorous, vulgar language. Or for standing up in disobedience. Or for demanding acknowledgement and action in whatever way you must.

Fuck Trump. But he’s just the ugly fake-gold mask they’ve put on this thing. Fuck all the GOP, fuck that blubbering, bristling frat boy judge, fuck McConnell, Ryan, Grassley, Collins, every last one of them. Fuck them for how they’ve shamed victims and helped dismantle democracy.

They will tell you to smile, that we need to get back to business, that we gotta heal the rift and blah blah blah — but that’s the desire of a savvy bully, who wants you to stop crying after he hit you, who wants you not to fight back. But you can cry. And you can fight back.

They can eat shit. All of them. They can eat a boot covered in shit.

Winter is coming, you callous fucknecks, you prolapsed assholes, you grotesque monsters, you racists and rapists and wretched abusers, you vengeful petty horrors.

Sidenote: some will tell you to be civil because our rage and scorn will fuel the other side, but fuck that double standard in both its ears.

“Well, if you hadn’t said those SASSY WORDS and demonstrated ANGER at our whittled-down democracy, I for a second might’ve been convinced not to eat this baby. But fie! Fie on you! Your incivility MADE me eat this baby!”

Spoiler warning: they were always gonna eat that baby.

Meanwhile, over on the other side of entitled apologists for the status quo, we’ve got Jonathan Haidt blaming both sides:

He’s ably rebutted by Gretchen Koch, but I have a shorter response: fuck Jonathan Haidt.

A nice day, topped with nuts

As it turns out, I’m traveling to Minneapolis today to have a pleasant time swanning about parks and such with my best beloved, so I’m probably going to drop by the ridiculous creationist talk by the Nuttings this evening. MCB 3-120 at 6:30. They always try to book rooms in the most sciencey building they can find, and MCB is short for Molecular and Cellular Biology, the antithesis of what they’ll be lying about.

“Chance vs Design” tonight — anyone want to bet they don’t understand the first and will present no evidence for the second?

Oh, and if you go, don’t expect me to draw down thunder and lightning on these frauds — I don’t debate, I’m just going to document, and later rebut the more egregious lies right here. Judging by commentary by an attendee at the previous two talks, I’ll have a lot to rebut.

Boghossian, Lindsay, and Pluckrose are simply incompetent hacks

There are many reasons why that inane fake article “study” was bad. Here’s a good summary from HJ.

But we also know bullshit gets published, with relatively little effort, in non-“grievance studies” journals. SCIgen is a program that automatically generates Computer Science papers. The authors were able to get one such paper accepted to a scientific conference in 2005. Eight years later, some researchers discovered that a whopping 120 SCIgen papers had been published across thirty conferences. That same year, John Bohannon submitted a paper on “medicinal lichen” that was machine translated from English to French and back again to 300 open-access journals; it was accepted in 157, and of the 36 submissions where peer reviewers caught the hoax a whopping 16 journals published the paper anyway. Not recent enough for you? While Boghossian and his two friends were toiling away on twenty papers, one person submitted an obvious hoax paper to fourteen biology journals; it got published in three journals and accepted in a further five.

Again, their core claim is that “grievance studies” journals are more prone to hoaxes than non-“grievance studies” journals. If we use my examples as controls, their hypothesis lacks sufficient evidence to be considered true; if we do not, then they don’t have control group and their hypothesis lacks sufficient evidence to be considered true.

Boghossian, Pluckrose, Lindsay, and Mounk do not have the science knowledge of an alert High School student. They should be deeply ashamed and laughed out of academia, instead of rewarded with wingnut welfare.

They used the same hatchet science denialists employ to criticize everything from evolution to climate to physics to medicine: find a few deficiencies — and that peer-review in general can be gamed is a recognized, ongoing problem — and use them to pillory an entire field of study. And like the denialists, they focus on one thing they don’t like, in this case feminism, and selectively criticize narrow, specific problems while generalizing to the whole. This is precisely the kind of game kooks play to claim that evolution is unsupported by evidence, that the earth’s climate isn’t changing, that cigarettes aren’t really that bad for you, and that the AMA is hiding a secret cure for cancer.

I agree. All of them have demonstrated a sophomoric understanding of science and a weird ideological bias that taints everything they do, and they’ve just earned a universal thumbs-down from academia.