Failing upwards

Bill Ackman is a hedge-fund billionaire who was very concerned that an MIT professor allowed a student to promote a pro-Palestine rally. He’s more worried about denying Palestinian civil rights than he is about known sexual harassers in the classroom, though.

Ackman is a major supporter of David Sabatini to the tune of millions of dollars per year. Sabatini, you may recall, was fired twice from major institutions and his attempt to be hired by NYU was aborted by huge demonstrations by the faculty and students there. He is not a good guy. He ran a party lab for dudebros.

In 2021, the Howard Hughes Medical Institute fired Sabatini, and the Whitehead Institute for Biomedical Research forced him out after an investigation by an outside law firm found he violated the institute’s sexual harassment and relationship policies. That investigation found that Sabatini conducted a clandestine sexual relationship with a woman scientist and asked her to meet him for sex on institute grounds. At the time, he was mentoring her in a program he directed while she launched a lab at the Whitehead. The investigation also found, among other behavior, that he created a lab culture that rewarded sexualized banter; implicitly threatened a faculty member who refused to make a place in his lab for a visiting woman scientist whom Sabatini later married; and created a “pervasive” fear of retaliation, for example implying there would be career consequences for lab members who reported unfavorably on him to the outside investigators or who discussed rumors that he was sexually pursuing a woman undergraduate from another institution.

I figured that with three strikes he was finally out, no matter how much money a rich boob threw his way. I even made a prediction: “He’ll go get a job in construction or pharmaceutical sales and we won’t have to worry about his unpleasant influence on academia anymore.”

I was wrong, so wrong. He’s starting up a new lab in Prague.

David Sabatini, the high-flying biologist who lost positions at three prominent U.S. institutions after breaching sexual misconduct policies, last month began a new job as a senior scientist at the Institute of Organic Chemistry and Biochemistry Prague (IOCB), a powerful arm of the Czech Academy of Sciences (CAS). The hire has divided Czech scientists and is likely to ignite debate about whether and when institutions should give second chances to those who commit sexual misconduct.

He’s like an antibiotic-resistant venereal disease. He keeps flaring up when you least expect it, and when you think you’ve finally beaten it back.

IOCB Director Jan Konvalinka said in a statement: “We believe that [Sabatini] has been punished enough for his previous actions and that the research community will be served best if this brilliant scientist returns to research.” He added that IOCB “will require that Dr. Sabatini follows the same high standards of conduct and respectful behavior that is expected from every other principal investigator.”

Yeah, that’s what the Whitehead, MIT, and NYU all said, too. When will people learn that “high standards of conduct and respectful behavior” aren’t in his repertoire?

Probably about the time that rich Republican jerks stop bankrolling him, I bet.

I guess you could argue that corporate capitalism is a kind of religion

Ken Ham is pissed off at this song from an upcoming Disney movie.

I know nothing about the movie, nor am I interested in seeing it (maybe my grandkids will enjoy it, I don’t know). I don’t think it will turn anyone into worshippers of Sol Invictus. All it is saying is that the world around us is pretty nifty.

Not in Ken Ham’s feeble mind, though.

Imagine if public school students in their science classes were encouraged to worship the sun. And yet this is happening! But how do they get away with it? Well, they just call worshipping the sun “science,” and then claim they can teach this “science” in the public schools! Really the Disney song mentioned above is all about worshipping the sun and stars.

That’s quite a leap, from a cheerful bit of fluff to a sinister plot to inculcate sun worship in public school classrooms. No one is teaching kids to pray to and worship natural objects in the universe.

By the way, he also doesn’t like Neil deGrasse Tyson.

“Our ancestors worshipped the sun. They were far from foolish. It makes good sense to revere the sun and stars because we are their children. The silicon in the rocks, the oxygen in the air, the carbon in our DNA, the iron in our skyscrapers, the silver in our jewelry—were all made in stars, billions of years ago. Our planet, our society, and we ourselves are stardust.”

That statement was made by Neil deGrasse Tyson in the Cosmos series he narrated. Evolutionists encouraged teachers to use this series in public school classrooms.

Oh, how awful: he was suggesting that pre-Christian people were not stupid, and were trying to understand the world as best as they could. Tyson is not an animist. He’s not saying it would be a good idea to worship rocks, but that we should try to understand why some people might have. Damn those public schools! They’re teaching tolerance and empathy! You won’t get any of that in a Ken Ham-approved homeschool.

He really is a fully coked-up conspiracy theorist.

I think it’s about time Christians woke up and understood that even though there are Christian missionaries in the public (Government) school system (and they need our prayers), by and large these schools are actually churches of atheism. Millions of students are being taught that all life and the universe arose by natural processes—by naturalism. But we need to call naturalism what it is—atheism.

Well, so, True Christians™ reject understanding of the natural world? There’s no difference between studying physics, chemistry, and biology and worshipping pagan gods and being an atheist? Good to know.

Please to stay out of education and politics, Ken.

Southern Adventist University is a pit of lies

If you’ve never heard of David Rives before, you’re fortunate: he’s a lesser creationist best known for the well-fed, smug, toothy smile of a prosperous real estate agent, and that he was formerly married to Jenna Ellis, former lawyer to Donald Trump who is now facing racketeering charges. It’s always sad when two hellbeasts get divorced.

Rives runs a creationist ministry with a YouTube channel in which he claims to be “changing the narrative.” He’s not. But I had to watch this video, title “Secrets of the Arachnids.” Before you jump in, though, I’ll warn you that the first 20 minutes is incredibly boring: he’s interviewing a dorky arachnologist named David Nelson, and aside from the vapid interjections of Rives, it’s mostly painless, and mostly the kind of stuff you might catch dorky me saying — he’s definitely enthusiastic about spiders. At about the 22 minute mark, though, I lose all sympathy for him.

We learn that David Nelson is a professor at Southern Adventist University in Chattanooga, Tennessee. Oh god. It’s one of those places.

The Biology and Allied Health Department fully supports a biblical six-day creation and developed the Origins Exhibit, a museum-quality display that showcases topics such as irreducible complexity of the cell, the geologic column, the flood, and dinosaurs.

Representatives of protein and peptide classes identified in spider venoms. Top panel: large proteins represented by Phospholipase D. Bottom two panels: short spider venom peptides divided into two major classes. The middle panel depicts selected neurotoxic ICK (inhibitor cystine knot) toxins (Versutoxin, Robustoxin and Huwentoxin-I). The lower panel shows representative antimicrobial peptides (Latarcin-II and Oxyopinin). Species names of spiders from which the components were isolated are indicated below the compound names. Secondary structures are indicated by colour (α-helices in blue, β-sheets in red, and turns in purple).

It’s a temple of misinformation. While I enjoyed the early part of his interview, when he’s talking about survey protocols and cool spider facts, it then goes off the rails when he starts talking about teaching a course in venoms and claiming that all venoms are flawed, degenerate versions of physiologically adaptive molecules, and that they support the biblical claim of a Fall and a loss of ‘information’. No, they’re not. If you read anything about The Biology and Evolution of Spider Venoms, you’d know that the components of a venom are complex and diverse. It’s not just a collection of failed phospholipase molecules, but a set of numerous, specialized molecules produced by duplication and divergence. It’s absurd to claim that this is a sign of biological decay.

Spider venom can contain up to 3000 different molecules, suggesting that the prospecting of all extant spider species could yield ~10 million venom components. Spiders therefore comprise a hyperdiverse lineage of predators with venom that is far more complex than that of most other animals.

Here’s a taste of the detail in the analysis of the structure of venoms. They are beautifully unique and specialized, and the Nelson gomer throws all the information away to claim it’s all about a loss of information. Yeah, guy, when you ignore all the information, it looks like a loss.

ICKs are the most abundant cysteine-stabilized peptides in nature: they are found in the venoms of many spiders and other animals, and have also evolved diverse functions in plants, fungi, bacteria and viruses (Undheim, Mobli & King, 2016). A fundamental obstacle hindering the evolutionary analysis of ICKs is the pseudoknot motif and its disulfide bonds, which are largely responsible for defining the tertiary structure of these peptides. Amino acid substitutions can therefore accumulate with little impact on structure, leading to profound diversity (Olivera et al., 1995; Sollod et al., 2005; Kozminsky-Atias & Zilberberg, 2012; Sunagar et al., 2013; Sunagar & Moran, 2015; Undheim et al., 2016). This challenge has been addressed recently by the application of ‘structural venomics’ (a combination of venom transcriptomics, proteomics and structural biology) in Hadronyche infensa to shed light on ICK evolution (Pineda et al., 2020). This approach showed that most ICK peptides are descendants of a single weaponized ICK lineage that underwent duplication and structural diversification, giving rise to a variety of peptides with elaborate ICK folds following their recruitment as venom components (Pineda et al., 2020). The ancestral ICK toxin was proposed either to contain a fourth disulfide bond that stabilized its β-sheet (lost in some descendants) or the typical three disulfide bonds with the fourth evolving independently at least twice (Pineda et al., 2020). Domain duplication would then explain the dICK peptides (Pineda et al., 2020). Structural venomics thus provides evidence that gene duplication is an important process in the evolution of spider venom and other venomous lineages. Similarly, gene duplication was proposed as an explanation for the evolution of αLTX in Latrodectus spp. (Gendreau et al., 2017; Schwager et al., 2017). However, it is important to note that the confident reconstruction of gene evolution processes requires genomic data. Results based exclusively on venomic data sets need to be interpreted with caution as assembly artifacts and overinterpretation can easily blur the evolutionary signature and lead to false assumptions. At least one ancient whole-genome duplication event is also thought to have occurred in the lineage leading to spiders and scorpions, providing the foundation for extensive neofunctionalization (Schwager et al., 2017).

You can’t talk about the evolution of anything without talking about neofunctionalization — that is, the emergence of new capabilities in evolving molecules. The science of venoms involves deducing where each toxin component came from, and dissecting the functional effect of each one.

Horizontal gene transfer has contributed to the evolution of some venom components, including PLD in the family Sicariidae (Cordes & Binford, 2018). PLD was traced to a single proteobacterial ancestor, from which it appears to have radiated widely, at least partially facilitated by horizontal gene transfer (Cordes & Binford, 2018). Horizontal gene transfer has also been proposed to explain the origin of αLTX, based largely on the complete genome sequence of Parasteatoda tepidariorum (Gendreau et al., 2017; Schwager et al., 2017).

What exactly does David Nelson teach in his venoms course? I am mystified. He seems to be building everything on flawed premises and an utter ignorance of the scientific literature. Does he hide PubMed from his students? Because two minutes with that would show that their professor is lying to them.

I haven’t even mentioned venom delivery systems. Does David Nelson teach that these represent a loss of function from a prelapsarian ideal?

Southern Adventist University ought to be shuttered and burned to the ground. Those poor students.

The problem with college athletics

It’s out of control. It’s insane. Look at this story out of Texas:

The concept of the college football coaching buyout reached its historical apex Sunday, when news broke that Texas A&M would dismiss Jimbo Fisher amid his sixth season as head coach. That dismissal would figure to entail the school and its boosters paying Fisher the remainder of his contract, which infamously totals around $76 million.

$76 million. What’s worse, they’re paying one man $76 million to stop working so they can hire someone else for an equivalent salary…a single salary that could instead have paid for over 700 full professors in real academic disciplines to work. And this is one guy! Imagine how much money is getting thrown down the rathole of recruiting and bloated coaching staffs and taking the players out for steak dinners every night. This is madness. This is college football.

This Jimbo Fisher guy never deserved that kind of extravagant salary, and even had a winning 6:4 season so far. You know what happened here: some absurdly rich asshole donor started complaining that “his” team wasn’t winning enough, and decided to meddle, so he could pretend to take credit when some young kid throws a touchdown pass.

This is no way to run a university.

The students don’t even notice because they’re all distracted by these phony rivalries. All they know is that to defend their honor their football team has to defeat some other football team in Texas, or Nebraska, or whereever. No, kids, that doesn’t matter.

Assembly Theory pops up again

This morning I was surprised to see Assembly Theory popping up all over in my social media. Did somebody find evidence for it? Did the authors clarify what their babble meant? No, nothing so interesting: another evolutionary biologist took a hard look at the original paper, and tried to figure out what Cronin was talking about.

In October, a paper titled “Assembly theory explains and quantifies selection and evolution” appeared in the top science journal Nature. The authors – a team led by Lee Cronin at the University of Glasgow and Sara Walker at Arizona State University – claim their theory is an “interface between physics and biology” which explains how complex biological forms can evolve.

The paper provoked strong responses. On the one hand were headlines like “Bold New ‘Theory of Everything’ Could Unite Physics And Evolution”.

On the other were reactions from scientists. One evolutionary biologist tweeted “after multiple reads I still have absolutely no idea what [this paper] is doing”. Another said “I read the paper and I feel more confused […] I think reading that paper has made me forget my own name.”

As a biologist who studies evolution, I felt I had to read the paper myself. Was assembly theory really the radical new paradigm its authors suggested? Or was it the “abject wankwaffle” its critics decried?

He highlights some of the weird stuff in the paper, like this observation that leapt out at me when I read it.

In the words of one Nature commenter: “Why so many creationist tropes in the first few sentences?”

Yeah, that was odd: either the author was so totally unaware of how creationists make really bad arguments, so he made one himself (the generous interpretation), or it was intentional, and he’s underhandedly trying to sneak creationist nonsense in the literature (the uncharitable interpretation). Either way it was a warning sign.

So the critic works through the paper, trying to answer the question, is it “abject wankwaffle” or not? The answer is phrased politely.

However, as a sweeping new paradigm aiming to unify evolution and physics, assembly theory appears – to me and many others – to be addressing a problem that does not exist.

“abject wankwaffle” it is!

Ayaan Hirsi Ali is a Christian now

In a totally unsurprising announcement, Ayaan Hirsi Ali renounces atheism and declares herself a Christian. I half-expected this to happen — she’s been working at the Hoover Institute with a lot of wealthy conservative Republicans, it was just going to take time to realize who was buttering her bread. I’ve read her autobiography, and it was clear that what drove her was in large part a resentment of the terrible Islamic authoritarians who controlled her life for so long. Well, now she’s come full circle and is identifying with a different set of terrible authoritarians.

As an atheist, I thought I would lose that fear. I also found an entirely new circle of friends, as different from the preachers of the Muslim Brotherhood as one could imagine. The more time I spent with them — people such as Christopher Hitchens and Richard Dawkins — the more confident I felt that I had made the right choice. For the atheists were clever. They were also a great deal of fun.

So, what changed? Why do I call myself a Christian now?

Part of the answer is global. Western civilisation is under threat from three different but related forces: the resurgence of great-power authoritarianism and expansionism in the forms of the Chinese Communist Party and Vladimir Putin’s Russia; the rise of global Islamism, which threatens to mobilise a vast population against the West; and the viral spread of woke ideology, which is eating into the moral fibre of the next generation.

Oh. So she has bought into the conspiratorial anti-woke nonsense, and the usual fear-based bullshit that is the foundation of most conservative thought. The communists are coming to get us! Our only hope is to follow a different authoritarian ideology!

But we can’t fight off these formidable forces unless we can answer the question: what is it that unites us? The response that “God is dead!” seems insufficient. So, too, does the attempt to find solace in “the rules-based liberal international order”. The only credible answer, I believe, lies in our desire to uphold the legacy of the Judeo-Christian tradition.

That phrase judeo-christian always sets off alarm bells in my head. Misrepresenting what atheism is about also doesn’t help.

That is why I no longer consider myself a Muslim apostate, but a lapsed atheist. Of course, I still have a great deal to learn about Christianity. I discover a little more at church each Sunday. But I have recognised, in my own long journey through a wilderness of fear and self-doubt, that there is a better way to manage the challenges of existence than either Islam or unbelief had to offer.

It’s Jeeeesus. Good luck with that, Ayaan Hirsi Ali.

By the way, nowhere in her long essay does she say a word about why Christianity is a good philosophy, other than that it’s a platform for fighting against Muslims and woke atheists.

Some people don’t understand free speech

Or how universities work. If they did, they’d see that this short video illustrates a perfectly normal, routine event. Someone asks to make an announcement in an MIT math class, waits politely for the professor to let them go, and then leads students in a chant as they march out of the classroom.

Oh yeah? So?

I’ve had students ask to announce an anti-abortion talk in my class. I am ferociously against that idea, but I let her speak…then I continued on.

I’ve had a student raise a hand in class in order to inform us all that there was a talk by a creationist in a local church that night. Fine. I wasn’t able to go to that one, but I’m sure it was entertaining.

I had students announce a protest march against the Iraq war…oh, wait, I agreed with that, and joined the march that afternoon.

I’ve had advocates for climate change protests, BLM, conservation, vegetarianism, gay & trans rights, etc. take a moment to make announcements in class. It’s fine.

I can’t emphasize enough how totally unremarkable this sort of thing is. Our students have diverse views, we’re at a goddamn university, and we encourage students to be aware, to be activists, to express themselves. What I see in that video is a tolerant professor giving a minute of time to let students voice their opposition to an ongoing violent political event, and they then left to protest.

And now assholes are showing that short clip and announcing that “wokeness” has gone too far, that anyone they disagree with is abusing free speech. I am unimpressed. I take that back — I am disgusted.

A cable problem explained

In the past, I have complained bitterly about the difficulty of getting reliable cables for Apple computers, and also about how ridiculously overpriced they all are. I may have been wrong. There’s a good reason for that.

Adam Savage takes apart several USB-C cables, from a $3 cheapie to a $10 Amazon to a $130 (!!!!!) official Apple cable, and I learned something new.

Whoa…those expensive cables are packed full of complex circuitry, which I did not expect. Back in the day, I used to make custom RS-232 cable all the time — cut open the cable, splay out all the little wires, solder them to the appropriate pin in the connector, and you were done. That’s all it was, was a wire-to-wire connection between two adapters. I don’t think I could make a USB cable, and it’s not only the teeny-tiny wires that would exceed my soldering ability, but I wouldn’t be able to cope with all the miniature ICs in there.

Some days…

I had to finish grading an exam for one class, and compose an exam for another class, which will soon bounce back demanding that I grade it. Also, this week is dedicated to advising, so I’ve had a stream of students coming to my office for assistance in getting ready for spring term. That’s been a real roller coaster: some students are sailing through, excelling at their courses, so we have to talk about what gets them excited, while other students are struggling, so we have to talk about what to do to get back on track and just plain survive. I’m starting to feel drained.

I mentioned that I’m not getting a sabbatical next year (but definitely will in 2025), so I’ve been working with the discipline to revise my schedule. There’s some happy news there: this spring I’ll be teaching ecological developmental biology, and then, in the fall, Developmental Biology! I am floored! For the first time in way too many years, I’ll be teaching courses in my specialty, and I’ll be doing it over two consecutive semesters! It almost makes up for not getting a sabbatical. Almost.

Now I have to get back to the student train — I have another scheduled appointment in 5 minutes, and then my cell bio class.