Went looking for Vikings at the Rune Stone Park, only found…

…spiders.

There are lots of things with the “Runestone” moniker attached in my area: Runestone Telecom Association, Runestone Apartments, Runestone Mobile Home Park, etc., etc., and there’s a park called Kensington Rune Stone Park just 40 minutes away from me. I decided to take a trip out there.

That’s a rather nice building to honor a fake carved rock supposedly left by Vikings visiting Minnesota in the 14th century. It’s empty now, probably due mostly to the pandemic, but it’s not clear what they do there — it contains a big empty meeting space, perhaps for lectures about Vikings. The Olaf Ohman farmhouse is there and a big barn and some nicely maintained grassy grounds. The notorious Runestone itself is not there — it has a separate museum of its own in Alexandria, 20 minutes away. It’s all rather embarrassing.

But we didn’t care we were there for spiders. We found a few!

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Gussying up creationism with math doesn’t make it valid

I’m trying to read this article, “Using statistical methods to model the fine-tuning of molecular machines and systems” by Thorvaldsen and Hössjer, and wondering why I even bother, and why the Journal of Theoretical Biology bothered to publish it, because a) it undermines its own premise in the introduction, b) it’s loaded with irrelevant math, c) it contains no observations or experiments, and d) at the end it devolves into the usual circle jerk of references to the usual suspects in the Intelligent Design community. I had to throw up my hands and give up. It’s just mathematicians juggling assumptions and numbers to come to the conclusion they want.

The one interesting aspect is that unlike the Discovery Institute gang, they do give clear explanations of what they mean by “design” and “fine tuning” — it’s just that, once you read them, you feel like telling them that their work is done, further noodling about is pointless. Maybe that’s why the Intelligent Design creationists try harder to fog over the meaning of the words they use?

Anyway, here’s the only interesting stuff in the whole thing.

The term fine-tuning is used to characterize sensitive dependences of functions or properties on the values of certain parameters (cf. Friederich, 2018). While technological devices are fine-tuned products of actual engineers and manufacturers who designed and built them, only sensitivity with respect to the values of certain parameters or initial conditions are considered sufficient in the present paper. We define fine-tuning as an object with two properties: it must a) be unlikely to have occurred by chance, under the relevant probability distribution (i.e. complex), and b) conform to an independent or detached specification (i.e. specific).

To which I would reply that a) unlikely events happen all the time, so mere measures of probability, especially after the fact, are of little consequence, and b) groovy, so does this mean you are going to provide an independent or detached specification for a specific evolutionary event? [Answer: No, they are not.] If your definition requires addressing two parameters, and at the very outset of your project you have to admit that you don’t have the second one and that playing mathematical games cannot provide it, then aren’t we done? That was the second paragraph of the whole article, which makes for a quick read, too.

But no, sorry, they go on.

The notion of design is also widely used within both historic and contemporary science (Thorvaldsen and Øhrstrøm, 2013). The concept will need a description for its use in our setting. A design is a specification or plan for the construction of an object or system, or the result of that specification or plan in the form of a product.

Yes, yes. I’ve been saying this for years. If you want to claim there was a design for an organism, show me the blueprint from which it was built, and I’ll believe you. If you go to Mars and find a set of billion year old program specifications for Project Mouse, laid out by the Martian designers, with a couple of thousand manuals that lay out the details of the biochemistry, physiology, and morphology of Mus musculus, then I’ll have to admit that you’ve got solid evidence that mice are the product of design. You’ve said it right there in your definition, that you have to have a specification or plan the precedes the product.

Except then they immediately waffle. All you need is the product itself, and then you get to infer the specification or plan. That makes no sense. I can find a pebble in my yard which is unique in all of its particulars, where every scrape and mark and fracture sets it apart from otherwise similar pebbles. The probability of that specific pebble having its specific constellation of attributes is minuscule. Are you going to try and tell me that therefore there is somewhere on file in the Great Designer’s filing cabinet a project laid out for Pebble, Minnesota, 21st Century, Myers yard, grey, roughly ovoid? You might believe that’s the case, but I’d like to see it.

Instead, we get a lesson in etymology. I had to laugh, this is so ridiculously irrelevant.

The very term design is from the Medieval Latin word “designare” (denoting “mark out, point out, choose”); from “de” (out) and “signum” (identifying mark, sign). Hence, a public notice that advertises something or gives information.

Great. So where’s the public notice? Somewhere in the main Megabrantis office which is open on Tuesdays, between 1 and 1:15pm, standard Vogsphere time?

The design usually has to satisfy certain goals and constraints. It is also expected to interact with a certain environment, and thus be realized in the physical world. Humans have a powerful intuitive understanding of design that precedes modern science. Our common intuitions invariably begin with recognizing a pattern as a mark of design. The problem has been that our intuitions about design have been unrefined and pre-theoretical. For this reason, it is relevant to ask ourselves whether it is possible to turn the tables on this disparity and place those rough and pre-theoretical intuitions on a firm scientific foundation.

Just once, please consider that our intuitions can be wrong, rather than struggling to find some mathematical justification for them.

Unfortunately, the paper is primarily about fine tuning, allowing them to ignore this problem, and they’re going to move on.

Fine-tuning and design are related entities. Fine-tuning is a bottom-up method, while design is more like a top-down approach. Hence, we focus on the topic of fine-tuning in the present paper and address the following questions: Is it possible to recognize fine-tuning in biological systems at the levels of functional proteins, protein groups and cellular networks? Can fine-tuning in molecular biology be formulated using state of the art statistical methods, or are the arguments just “in the eyes of the beholder”?

Yes. We are quite confident that biological organisms have been fine tuned by natural selection. Is that what you mean?

There’s no point in worrying about it, though, because after I read the following sentence I threw my hard copy of the paper in the trash.

The chances that the universe should be life permitting are so infinitesimal as to be incomprehensible and incalculable.

But…but…if they’re incalculable, then how did you determine that they are infinitesimal? Jesus. Creationist mathematicians.

My brain unconsciously turned to spiders

Chuck Wendig has a list of ten things you can do to persist “in this epoch of syphilitic dipshittery”. It’s not bad. I’ve been following this advice without knowing it for a while. But he left one off.

11. Do your spiders. That’s right. Find a new obsession, the more weird and off the wall it is, the better. Just concentrate for a while every day on it, turn it into an art and science, and identify with your spiders. Because I tell you, it doesn’t matter what it is, it’s healthier and saner than the politics in your country right now.

So that’s my plan for today. I shall retire to my lab and office, fiddle about with some new apparatus, fuss over my spiders, and someday, when the time is right, we shall conquer the world and end the reign of foolish primates.

You’ve all got your spiders, or spider-substitutes. What are they? What will you do today to expand your domain?

I guess we’re in the midst of tornado season

June and July are the peak months for tornadoes in the upper midwest, and June was a bit of a bust, so I guess we can expect July to compensate. One ripped through Dalton the other day, which is less than an hour north of us.

Yikes. To put it in perspective, though, in the 20 years I’ve been here, I haven’t seen one, although they have come close, and I’ve seen the sky turn greenish.

I rather like the woman in the video who tells the yammering guy to STFU, at least.

Cultivating a British flavor of narrow-mindedness

Trying to figure out why so many TERFs are British, I think this answer hits the nail on the head.

The answer lies in part to the coalescence of a certain set of ideas in a very specific circle of voices in the early 21st century — voices that later went on to hold high profile positions in much of the U.K.’s print and broadcast media.

I’m referring here to the U.K. Skeptics movement of the early 2000s. Despite the fact that it was basically a loose network of people who were far too impressed with themselves for not believing in astrology and homeopathy, they have an outsized legacy. The movement consisted largely of groups meeting in pubs and organising talks promoting a specific brand of scientific skepticism and concerned primarily with the “debunking” of alternative medicine and pseudoscience. So far, so niche, but there is compelling evidence that suggests that both the ideological basis and some of the specific proponents of U.K. skepticism in the noughties are implicated in the spread of transphobic thinking into the mainstream media in this country.

While claiming to be the country’s foremost critical thinkers, the group was riddled with anti-humanities bias and a fetish for a certain kind of “science” that it held to reveal a set of immutable principles upon which the world was built with almost no regard whatsoever for interpretative analysis based on social or historical factors. Part of this mode of thinking was an especially reductivist biologism: the idea that there are immutable realities to be found in our DNA, and if we just paid enough attention to Science and stopped trying to split hairs and discover meaning over in the superfluous disciplines of the humanities, then everything would be much simpler. It’s precisely this kind of biological essentialism — which skirts dangerously close to eugenics — that leads people to think they can “debunk” a person’s claim to their gender identity, or that it should be subjected to rigorous testing by someone in a lab coat before we can believe the subject is who they say they are.

I saw the same thing in US skeptics, of course. But there was something fundamental going on that is also reflected in the British school of evolutionary biology, represented by Maynard Smith and Dawkins, that totally embraced reductive explanations and adaptationism, vs. the American subset led by Lewontin and Gould, who fiercely opposed eugenics and detested the arrogance of thinking biology could be reduced to a catalog of alleles. My experience may also be colored by the fact that there were several prominent UK skeptics (at least, I was told over and over that they were big names) who I had to ban here because they were persistently obnoxious and insistent that there are only two sexes/genders because “biology”.

Then there’s the outcome of all this activity by bigots claiming the mantle of science — some people actually believed them.

Tracey King, a skeptic activist who credits herself with establishing American-style organized skepticism in the U.K., has pointed out that the movement collapsed in the last decade. She attributes this to some good reasons (turns out it was full of sexists, which the rise of social justice concerns helped bring to light.) But these voices did not go away; many of the figures who made up the movement are now prominent voices at one level or another. Helen Lewis, for example, is the deputy editor of the center-left political magazine the New Statesman, and has promoted a barrage of anti-trans articles. Julie Bindel at the Guardian and elsewhere has a well-documented history of transphobia.

Then there’s Graham Linehan, a formerly beloved high-profile comedy writer who has recently been given a warning by police for directly harassing trans women online. Imagine if Larry David or Jerry Seinfeld suddenly started a social media hate campaign against a particular group of people that took up most of their time and you had to accept that was just part of your reality now. It feels a bit like that.

I met Linehan — he came to one of my talks in Dublin. Then, I was quite pleased to see him, but now…oh god what kind of wanker was I inspiring/being inspired by?

By the way, Seinfeld has been a loud voice whining about PC culture on college campuses — if I were him, I’d be wondering why smart young people no longer find him funny, rather than blaming it on a contrived slogan like “political correctness” — but at least he hasn’t carried his obsession as far as Linehan has.

Pratfalls are entertaining, right?

And now for something different. I wanted to experiment with this streaming thing all the cool kids do, so I’m trying out OBS and playing around with YouTube, and the easiest thing to do is to fire up Minecraft and see if I can put it online. Watch! I’ll probably screw up some settings! If it works, you can count on me to die multiple times! You can yell at me over chat!

I don’t know how long I’ll play, since I’m mainly interested in figuring out the mechanics, but if you encourage me to do some stupid thing, I might keep plodding along from disaster to disaster. That’ll be fun, right?

(If you’re wondering about details, this is under Linux, using a Logitech webcam, a Yeti microphone, and OBS software. It should work, with the only question being the competence of the bozo setting it up.)

Hey, that went surprisingly well. All the software worked, I didn’t die in Minecraft, I found a good location to build a house. What could be better? Well, the audio. I was getting an annoying hiss throught, and it would crackle and break up if I spoke too loudly. Maybe I’ll try it again next week, after I hammer out some of the sound problems.

How about some happy news?

The University of Minnesota Morris has achieved carbon neutrality!

This year the University of Minnesota Morris achieved a new milestone in its journey toward complete campus carbon neutrality. The campus is now fully carbon neutral in electricity because of on-site clean energy systems.

Over the past decade UMN Morris has built an on-site, community-scale, clean energy platform. In 2019 Environment America recognized that UMN Morris produced the most on-site electricity per student in the United States. The majority of campus power, about 60%, is generated by two University of Minnesota-owned 1.65 megawatt wind turbines. Additional green electricity is generated by several solar photovoltaic systems and a back-pressure steam-turbine at the biomass gasification plant.

I’ve noticed the solar panels sprouting up around campus, so it’s good to see they’ve made significant progress in making our university a bit more green.

The history of genetics is too often a horror story

I had already known that the number of human chromosomes had been incorrectly reported as 48 (it’s actually 46), and that observers maintained that number for decades, seeing what they expected to see. I’ve used it as an example for years to tell students to clear their heads of preconceptions when making observations, trust what you see, and report your measurements as accurately as you can, because this tendency favoring confirmation bias can corrupt science surprisingly easily. It sounds like a relatively benign example: oops, early investigator makes a mistake counting chromosomes (I’ve done some chromosome work, it’s easy to do), and the initial observation gets perpetuated through the literature until superior techniques make the correct value obvious. Ha ha, don’t do that.

Now Dan Graur digs into the details of the mistake, and it turns out to be a goddamn horror story. There are more lessons here than I thought.

The guy who made the mistake was named Theophilus Painter, and he seems to have stumbled upwards throughout his career by being a terrible person.

The first horror: the specimens he used to make those initial chromosome counts were human testicles lopped off prisoners in an asylum. They were castrated for the crime of excessive masturbation. The methods discuss some grisly details I really didn’t need to know.

“The material upon which this study is based was obtained from three inmates of the Texas State Insane Asylum through the interest and cooperation of Dr. T. E. Cook, a physician at that institution. Two of these individuals were negroes and one was a young white man. In all three cases, the cause for the removal of the testes was excessive self abuse… The operation for the removal of the testes was made, in all three cases, under local anesthesia. An hour or two prior to the operation, the patients were given hypodermic injections of morphine in order to quiet them. This was followed by local injections of Novocain in the operating room. None of the patients exhibited any interest or excitement during the operation, nor did they show any signs of pain except when the vas deferens and the accompanying nerves were cut. One of the negroes went to sleep during the operation.”

Yikes. I guess mutilation of your patients was a routine practice in 1923. No big deal, Negroes don’t feel pain.

The second horror: as you might guess from the passage above, the whole affair was soaking in racism. Painter got the same erroneous chromosome count from all 3 of his victims, but always reported the count separately for his black and white subjects. There may also have been confirmation bias in Painter’s work, because more recent examination of his slides, which still exist, reveal that his methods were a cytological mess and it’s difficult to count chromosome numbers from them at all.

The third horror: Painter later got appointed to the presidency of the University of Texas because he was a reliably negligent creature who would happily turn a blind eye to blatantly discriminatory admission policies, and would allow segregation to continue.

Read Graur for all the details. I’m just dismayed that a point I’ve always used casually as an example of a simple error with long-term consequences is now going to have to be presented as a deeper point about bad science being used for evil. Oh, well, students should know how genetics can be misused for wicked purposes, and here’s yet another case.

Looks exactly like my office

I’m still trying to work out the biology of nest building in my spiders — I’ve got some that assemble cunning little nests out of wood shavings, and some that do not. Someday I’ll have to figure out whether this is a different species from P. tepidariorum or not.

Cute, hey? I’ve been looking at spider architecture for a while, and am rather impressed with their work.

I suspect it might be P. tabulata, but I’ve got to do more experiments to be sure. I say more about it on my Patreon page.