Science needs specific, informed, productive criticism

Professor Dave demolishes Sabine Hossenfelder.

I feel that. The topic of my history class last week and this week is about bias in late 19th/early 20th century evolutionary biology, and how we have to be critical and responsible in our assessment of scientific claims. It’s tough, because I’m strongly pro-science (obviously, I hope?) but I keep talking about dead ends and errors in the growth of a scientific field, and I have to take some time to reassure the students that our only hope to correct these kinds of problems is…science. I also have to explain that the way the errors are discovered is…science, again.

I’m not specifically interested in Sabine Hossenfelder — I don’t watch her videos, not even the ones that might contain good information — but I am concerned with the general problem of how anti-science propaganda manages to advance the causes of dogma. If science gets something wrong, as it does sometimes, it does not mean that superstition or bigotry are right. Raging against the whole of the scientific establishment and the scientific method is how you get RFK Jr put in charge of the NIH. I don’t think that even Hossenfelder believes that will be an improvement.

Another step in the evolution of multicellularity

I’m not a fan of phys.org — they summarize interesting articles, but it’s too often clear that their writers don’t have a particularly deep understanding of biology. I wonder sometimes if they’re just as bad with physics articles, and I just don’t notice because I’m not a physicist.

Anyway, here’s a summary that raised my hackles.

Chromosphaera perkinsii is a single-celled species discovered in 2017 in marine sediments around Hawaii. The first signs of its presence on Earth have been dated at over a billion years, well before the appearance of the first animals.

A team from the University of Geneva (UNIGE) has observed that this species forms multicellular structures that bear striking similarities to animal embryos. These observations suggest that the genetic programs responsible for embryonic development were already present before the emergence of animal life, or that C. perkinsii evolved independently to develop similar processes. In other words, nature would therefore have possessed the genetic tools to “create eggs” long before it “invented chickens.”

First two words annoyed me: Chromosphaera perkinsii ought to be italicized. Are they incapable of basic typographical formatting? But that’s a minor issue. More annoying is the naive claim that a specific species discovered in 2017 has been around for a billion years. Nope. They later mention that it might have “evolved independently to develop similar processes”, which seems more likely to me, given that they don’t provide any evidence that the pattern of cell division is primitive. It’s still an interesting study, though, you’re just far better off reading the original source than the dumbed down version on phys.org.

All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of how and when this process first emerged remain elusive. Here, by combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii—a close relative that diverged from animals about 1 billion years ago—undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous and palintomic developmental program of C. perkinsii hint that such multicellular development either is much older than previously thought or evolved convergently in ichthyosporeans.

Much better. The key points are:

  • C. perkinsii is a member of a lineage that diverged from the line that led to animals about a billion years ago. It’s ancient, but it exhibits certain patterns of cell division that resemble those of modern animals.
  • Symmetry breaking is a simple but essential precursor to the formation of different cell types. The alternative is equipotential cell division, one that produces two identical cells with equivalent cellular destinies. Making the two daughter cells different from each other other opens the door to greater specialization.
  • Palintomic division is another element of that specialization. Many single-celled organisms split in two, and each individual begins independent growth. Palintomic division involves the parent cell undergoing a series of divisions without increasing the total cell volume. They divide to produce a pool of much smaller cells. This is the pattern we see in animal (and plant!) blastulas: big cell dividing multiple times to make a pile of small cells that can differentiate into different tissues.
  • Autonomy is also a big deal. They looked at transcriptional activity to see that daughter cells had different patterns of gene activity — some cells adopt an immobile, proliferative state, while others develop flagella and are mobile. This is a step beyond forming a simply colonial organism, is a step on the path to true multicellularity.

Cool. The idea is that this organism suggests that single-celled organisms could have acquired a toolkit to enable the evolution of multicellularity long before their descendants became multicellular.

I have a few reservations. C. perkinsii hasn’t been sitting still — it’s had a billion years to evolve these characteristics. We don’t know if they’re ancestral or not. We don’t get any detailed breakdown of molecular homologies in this paper, so we also don’t know if the mechanisms driving the patterns are shared.

I was also struck by this illustration of the palintomic divisions the organism goes through.

a, Plasma membrane-stained (PM) live colonies at distinct cell stages, highlighting the patterned cleavage divisions, tetrahedral four-cell stage and formation of spatially organized multicellular colonies (Supplementary Video 5). b, Actin- (magenta) and DNA-stained (blue) colonies at distinct cell stages showcasing nuclear cortical positioning, asymmetrical cell division (in volume and in time) and the formation of a multicellular colony. This result has been reproduced at least three independent times.

Hang on there : that’s familiar. D’Arcy Wentworth Thompson wrote about the passive formation of cell-like cleavage patterns in simple substrates, like oil drops and soap bubbles, in his book On Growth and Form, over a century ago. You might notice that these non-biological things create patterns just like C. perkinsii.

Aggregations of oil-drops. (After Roux.) Figs. 4–6 represent successive changes in a single system.

Aggregations of four soap-bubbles, to shew various arrangements of the intermediate partition and polar furrows.

An “artificial tissue,” formed by coloured drops of sodium chloride solution diffusing in a less dense solution of the same salt.

That does not undermine the paper’s point, though. Multicellularity evolved from natural processes that long preceded the appearance of animals. No miracles required!

If it’s not one thing, it’s another

It was hard to get motivated this morning — Fridays are typically low attendance days in the classroom, and I had worked hard to get today’s topic condensed down into a lot of digestible information (we’re talking about the rediscovery of Mendel, the biometrician and Mendelians arguing with each other). I had a presentation that was pretty tight and I thought would help make the conflict comprehensible to a group of liberal arts majors, none of whom are biology majors.

So I get to class today, and was pleasantly surprised to see that I had 80% attendance, which is kind of a miracle. I tell you, standing at the front of a classroom with only 3 students who don’t really appreciate the work you put in to the class is mighty depressing. So I was temporarily heartened that maybe this lecture wouldn’t go to waste, I fired up my laptop and the projector and got ready to tell this exciting story…and the projector is glitched out. It’s not connecting to anything, and is showing me a message that the projector and microphones were not receiving any data since 5:21pm yesterday. Isn’t technology nice that it has become so sophisticated that it can tell you precisely when it broke down?

I fumbled with it for about 15 minutes — that was the show today, watching the old geezer prof toggling switches and poking at a keyboard in front of the class, and seeing everything fail. I ended up giving up, giving them a brief oral summary of the history of biology from 1900-1915, telling them I’ll give them all the details on Monday, and sending them home early. So many smiles from the students! I didn’t tell them that I don’t find that encouraging at all.

Now I’m sitting in an empty classroom waiting for the IT people to show up. At least I can cheer myself up by thinking, hey, this isn’t the worst thing to happen this week.

Some days, I wonder why I’m doing this

Yes. But they’ll feel like they’re the one who failed.

Today, I had 3 students (out of 11) show up for what I thought was a scintillating talk about the immediate aftermath of publishing The Origin. Wilberforce and Huxley! Huxley humiliating Owen on the hippocampus minor question! Fleeming Jenkins’ extremely awkward question! Darwin’s epic genetics failure! How can you not want to discuss these dramatic events?

Maybe I’m not as scintillating as I thought. How are these students going to learn anything if they don’t keep up? Less significantly, how do they expect to pass?

Retirement looks ever more attractive.

P.S. I should mention that my entire class is not at risk of failing. Some are. Others may be working on a lower grade than they want.

Today I’m doing a “fool’s experiment” in the classroom

Fridays are the worst, from a teacher’s perspective, and Mondays are great. Students start out the week full of enthusiasm and slowly deflate, so today I’ve only got 50% attendance…and that’s typical. I try to pack Mondays with all the deep information, while on Fridays I try to do something different.

We’ve been talking about Darwin this week. I’ve given them an in-class exercise to browse through the Darwin project and begin to put together a short essay. Here are their instructions.

In your next essay, you’re going to be a real historian: I want you to read a few samples of primary historical references from Charles Darwin, and interpret and explain what he is writing about.

The Darwin Correspondence Project (https://www.darwinproject.ac.uk/) is a massive archive of letters to and from Charles Darwin, containing about 15,000 documents that have all been indexed and made publicly available. I want you to dive into this pile of letters, pluck out a few, and read them carefully. You may have to do additional research to figure out who these long dead people were, but the Darwin Project has actually done a lot of that work for you.

Write a 750 word essay that explains the context and meaning of the letters you choose. Unlike most scientific writing, this kind of essay encourages quoting your source — but don’t use up more than 250 words in direct quotes.

You get to choose the topic of the letters. Some might contain heavy scientific arguments, others might be friendly chit-chat, some are questions about that flower you were supposed to mail to me. They’re all good and interesting! Peek into the mind of a famous scientist, and you’ll find both deep revelations and mundane conversation.

In class: before you go, summarize to the group what you intend to write about, or tell us something interesting that you found.

I’m in class, working in parallel with them, and occasionally interrupting to get an idea of what they’re focusing on. I was most interested in Darwin’s “fool experiments“. These were experiments where you figured that it would never work, or that the answer would be obvious, but you go ahead and do the experiment anyways.

‘I love fools’ experiments. I am always making them’, was one of the most interesting things the zoologist E. Ray Lankester ever heard Darwin say. ‘A great deal might be written as comment on that statement’, Lankester later recorded, but he limited himself to stating that ‘the thoughts which it suggests may be summed up by the proposition that even a wise experiment when made by a fool generally leads to a false conclusion, but that fools’ experiments conducted by a genius often prove to be leaps through the dark into great discoveries.’

That’s a really good idea. I should go do a fool’s experiment this afternoon, maybe I’ll be surprised.

My students are right now digging into Darwin’s religious beliefs, his love life, his speculations about the age of the earth, and are going to give me the details next week. This should be fun.

The things we get away with at a liberal arts university…poetry in a science class? Tsk.

I am struggling with student engagement in all of my classes: poor attendance, poor participation, all those horribly negligent bugaboos that make it hard to teach. So here we are, halfway through the term almost, and I’m trying to shake things up.

I’m teaching a course titled “The History of Evolutionary Thought,” which is also a writing-enriched course — I’m expected to spend half the class time, approximately, teaching writing skills. I consider that permission to get experimental at times. This past week I lectured on the history of geology, Hutton through Lyell, so today I made them sit down and do a writing exercise.

We read poetry.

Can I do that in a science building, in a science course? You betcha. I did. I made them think about a poem about James Hutton. I gave them these instructions:

The idea of Deep Time inspired many writers, and some of them are poets. Today, I want you to write a paragraph on this poem. You can
• interpret some aspect of the poem
• write about the virtue of poetry to science
• explain how it makes you feel
• express your own ideas about Deep Time
• write your own poem!

And here’s the poem!

JAMES HUTTON LEARNS TO READ THE
HIEROGLYPHICS OF THE EARTH
by Ron Butlin
 
Woken once too often by the rattle-clatter
of tumbril wheels on cobbles, the click . . . click . . .
click of distant knitting needles,
James Hutton decided never to go
to sleep again.
 
Then, by the light of several Edinburgh Council moons
(spares, in case the heavens were taken over
by the church), he tip-toed past storm-wrecked
Holyrood Abbey, went striding down
unimagined corridors,
through undreamt-of walls and doors where
Scottish Hope would one day
be cemented into place
(the bars across its parliament windows
wooden, just in case).

The Park . . . Salisbury Crags . . .
 
where several hundred million years ago,
the Earth had cracked itself wide open –
*
Detailed as a map of Man’s undiscovered self,
zigzag Time lies flat-packed,
for everyone to see . . .
 
Stacked magma, olivine, dolerite chilled to glass,
eternity crushed to lines of slowly
spelled-out hieroglyphics, and cut
in blood-red haematite.
 
. . . and Hutton sees it. He’s the first!

First to know he walks upon an ancient ocean floor
(God’s Flood, the merest puddle in all that vastness).
First to hear the stone-hard heartbeat pound-pound-
pounding out Existence.
 
Elsewhere, Revolution has taken to the streets
with an accusation and a scream,
a guillotine-swish . . .
French clocks run backwards to Year One.
 
Sunday 23rd October 4,004 BC?
All in the blink of a biblical eye! says Hutton.
*
Meanwhile, you and I continue turning
on our axis to the tick . . .
tick . . . tick of Time that never
started Once upon a . . .
And will surely never, ever –
 
Ah, these strata, these infinities glimpsed between!

I made them ponder and write for 25 minutes, and then we had a discussion. I think it went well. They were wide awake, at least!

Next week, I’m talking about pre-Darwinian ideas about biological change. Maybe I should read them one of Erasmus Darwin’s poems? Or maybe not — they’re awfully suggestive, and I don’t want to end up like Joe Gow.

Jonathan Wells is dead

Wells was one of the worst liars at the Discovery Institute, which is saying a lot. His pals out there in Seattle are writing his praises, of course; you won’t be surprised that they don’t understand why Wells’ books were loathed. Here’s Casey Luskin, who inevitably gets everything wrong.

A lot of people hated Jonathan, not because he was a hateworthy person, but because of the bad news he delivered about their scientific arguments. His ideas threatened their paradigm, and he wasn’t afraid to say so. But he didn’t hate back. He was a kind and caring person who used his gifts to make an immense impact, helping to reform junk science that had bloated evolution education worldwide. For all these reasons, Dr. Jonathan Wells will not be forgotten anytime soon. By his many friends, readers, and others who have benefited from his research, and of course by his loving family, he will be greatly missed.

He did not deliver bad news about scientific arguments; he didn’t understand, or pretended not to understand, the science he was criticizing. Everything he wrote was a misrepresentation. He didn’t reform junk science, he vomited up books that were nothing but junk science. I am confident that he wasn’t just ignorant, but that he intentionally, willfully, and maliciously lied about the science.

He was an intelligent man who got a Ph.D. in religious studies from Yale, and then got a second Ph.D. in cellular and developmental biology from the University of California Berkeley. There’s rarely ever a good reason to get a second Ph.D., and Wells had the worst reason ever: he had become a Moonie, and he got the second degree at the behest of his church so that he would be better equipped to destroy Darwinism.

Father’s [Rev. Moon’s] words, my studies, and my prayers convinced me that I should devote my life to destroying Darwinism, just as many of my fellow Unificationists had already devoted their lives to destroying Marxism. When Father chose me (along with about a dozen other seminary graduates) to enter a Ph.D. program in 1978, I welcomed the opportunity to prepare myself for battle.

Yeah, he was one of those misguided people who went through a research program not to learn anything, but to get a few letters after his name so he could pretend to be an authority. He also dishonored Berkeley with a badge of shame; it is appalling that someone so dishonest and so committed to distorting the science could fool the research scientists at that prestigious university.

He distorted every idea he touched. Larry Moran thoroughly debunked his treatment of junk DNA, for my part, I wrote about how he constantly botched and misinformed people about developmental biology. Here’s an example of one of my posts in which I wasted my time dissecting the glurge of garbage pouring out of his Moonie brain.

The next person–apparently a professor of developmental biology–objected that the film ignored facts showing the unity of life, especially the universality of the genetic code, the remarkable similarity of about 500 housekeeping genes in all living things, the role of HOX genes in building animal body plans, and the similarity of HOX genes in all animal phyla, including sponges. 1Steve began by pointing out that the genetic code is not universal, but the questioner loudly complained that 2he was not answering her questions. I stepped up and pointed out that housekeeping genes are similar in all living things because without them life is not possible. I acknowledged that HOX gene mutations can be quite dramatic (causing a fly to sprout legs from its head in place of antennae, for example), but 3HOX genes become active midway through development, 4long after the body plan is already established. 5They are also remarkably non-specific; for example, if a fly lacks a particular HOX gene and a comparable mouse HOX gene is inserted in its place, the fly develops normal fly parts, not mouse parts. Furthermore, 6the similarity of HOX genes in so many animal phyla is actually a problem for neo-Darwinism: 7If evolutionary changes in body plans are due to changes in genes, and flies have HOX genes similar to those in a horse, why is a fly not a horse? Finally, 8the presence of HOX genes in sponges (which, everyone agrees, appeared in the pre-Cambrian) still leaves unanswered the question of how such complex specified genes evolved in the first place.

The questioner became agitated and shouted out something to the effect that HOX gene duplication explained the increase in information needed for the diversification of animal body plans. 9I replied that duplicating a gene doesn’t increase information content any more than photocopying a paper increases its information content. She obviously wanted to continue the argument, but the moderator took the microphone to someone else.

It blows my mind, man, it blows my freakin’ mind. How can this guy really be this stupid? He has a Ph.D. from UC Berkeley in developmental biology, and he either really doesn’t understand basic ideas in the field, or he’s maliciously misrepresenting them…he’s lying to the audience. He’s describing how he so adroitly fielded questions from the audience, including this one from a professor of developmental biology, who was no doubt agitated by the fact that Wells was feeding the audience steaming balls of rancid horseshit. I can’t blame her. That was an awesomely dishonest/ignorant performance, and Wells is proud of himself. People should be angry at that fraud.

I’ve just pulled out this small, two-paragraph fragment from his longer post, because it’s about all I can bear. I’ve flagged a few things that I’ll explain — the Meyer/Wells tag team really is a pair of smug incompetents.

1The genetic code is universal, and is one of the pieces of evidence for common descent. There are a few variants in the natural world, but they are the exceptions that prove the rule: they are slightly modified versions of the original code that are derived by evolutionary processes. For instance, we can find examples of stop codons in mitochondria that have acquired an amino acid translation. You can read more about natural variation in the genetic code here.

2That’s right, he wasn’t answering her questions. Meyer was apparently bidding for time until the big fat liar next to him could get up a good head of steam.

3This implication that Hox gene expression is irrelevant because it is “late” was a staple of Wells’ book, Icons of Evolution and the Politically Incorrect Guide to Darwinism and Intelligent Design. It’s a sham. The phylotypic stage, when the Hox genes are exhibiting their standard patterns of expression, of humans is at 4-5 weeks (out of 40 weeks), and in zebrafish it’s at 18-24 hours. These are relatively early events. The major landmarks before this period are gastrulation, when major tissue layers are established, and neurulation, when the neural tube forms. Embryos are like elongate slugs with the beginnings of a few tissues before this time.

4What? Patterned Hox gene expression is associated with the establishment of the body plan. Prior to this time, all the embryonic chordate has of a body plan is a couple of specified axes, a notochord, and a dorsal nerve tube. The pharyngula stage/phylotypic stage is the time when Hox gene expression is ordered and active, when organogenesis is ongoing, and when the hallmarks of chordate embryology, like segmental myotomes, a tailbud, and branchial arches are forming.

5Hox genes are not non-specific. They have very specific patterning roles; you can’t substitute abdominal-B for labial, for instance. They can be artificially swapped between individuals of different phyla and still function, which ought, to a rational person, be regarded as evidence of common origin, but they definitely do instigate the assembly of different structures in different species, which is not at all surprising. When you put a mouse gene in a fly, you are transplanting one gene out of the many hundreds of developmental genes needed to build an eye; the eye that is assembled is built of 99% fly genes and 1% (and a very early, general 1%) mouse genes. If it did build a mouse eye in a fly, we’d have to throw out a lot of our understanding of molecular genetics and become Intelligent Design creationists.

Hox genes are initiators or selectors; they are not the embryonic structure itself. Think of it this way: the Hox genes just mark a region of the embryo and tell other genes to get to work. It’s as if you are contracting out the building of a house, and you stand before your subcontractors and tell them to build a wall at some particular place. If you’ve got a team of carpenters, they’ll build one kind of wall; masons will build a different kind.

6No, the similarity of Hox genes is not a problem. It’s an indicator of common descent. It’s evidence for evolution.

7Good god.

Why is a fly not a horse? Because Hox genes are not the blueprint, they are not the totality of developmental events that lead to the development of an organism. You might as well complain that the people building a tarpaper shack down by the railroad tracks are using hammers and nails, while the people building a MacMansion on the lakefront are also using hammers and nails, so shouldn’t their buildings come out the same? Somebody who said that would be universally regarded as a clueless moron. Ditto for a supposed developmental biologist who thinks horses and flies should come out the same because they both have Hox genes.

8You can find homeobox-containing genes in plants. All that sequence is is a common motif that has the property of binding DNA at particular nucleotide sequences. What makes for a Hox gene, specifically, is its organization into a regulated cluster. How such genes and gene clusters could arise is simply trivial in principle, although working out the specific historical details of how it happened is more complex and interesting.

The case of sponges is enlightening, because they show us an early step in the formation of the Hox cluster. Current thinking is that sponges don’t actually have a Hox cluster (the first true Hox genes evolved in cnidarians), they have a Hox-like cluster of what are called NK genes. Apparently, grouping a set of transcription factors into a complex isn’t that uncommon in evolution.

9If you photocopy a paper, the paper doesn’t acquire more information. But if you’ve got two identical twins, A who is holding one copy of the paper, and B who is holding two copies of the same paper, B has somewhat more information. Wells’ analogy is a patent red herring.

The ancestral cnidarian proto-Hox cluster is thought to have contained four Hox genes. Humans have 39 Hox genes organized into four clusters. Which taxon contains more information in its Hox clusters? This is a trick question for Wells; people with normal intelligence, like most of you readers, would have no problem recognizing that 39 is a bigger number than 4. Jonathan Wells seems to have missed that day in his first grade arithmetic class.

It still infuriates me that a guy with a Ph.D. in developmental biology from Berkely would ask, if flies have HOX genes similar to those in a horse, why is a fly not a horse? Because the Hox genes only trigger the deployment of downstream genes of the animal, ya idjit.

Casey Luskin is wrong. I didn’t hate Wells personally — I never met him — but I did hate his lies, of which there were many, whole books worth of ’em. Good riddance to lying scum.

Behold, the worst teacher in the world!

If you see this face coming, kick him or spit on him or otherwise scorn him. He’s terrible.

I’m having a bad semester. I’m teaching my intro biology course, which is small and ideally sized with 10 students, and every day is a trial. I go in prepared; I’m cheerful and friendly, I think; I’m working on the shaggy Santa Claus look; I’ve got lectures with frequent pauses and breaks where I encourage discussion; I think it’s an interesting topic. I’m talking amiably, and I ask the class a question — it can be as simple as “what are the results of crossing two heterozygotes?” or more open-ended, like “what is your opinion of IVF?” and it’s always the same result: dead silence, stony faces, everyone avoiding my eyes. It’s killing me. Am I intimidating? Boring? Hideous? Should I wear a bag on my head? I keep trying to get them engaged, and all I’m getting for my troubles is flop sweat.

These are not stupid students, either. I gave them a quiz last week, the mean was somewhere in the low 80s, so I know they’re understanding the material. They just don’t want to talk to me.

I’m thinking that maybe I should try some in-class ice breakers next week, and see if I can get them more active. Anyone got any good suggestions? I’m getting desperate.

Alternatively, I pick up a fifth of vodka and numb myself before walking into the classroom, because the strain is getting to me.*

*Not actually an option. I gave up all alcohol during the pandemic.

If you’re in the neighborhood…

On Thursday, 12 September, at 2:30, I’m joining forces with another class to drag our freshman students outside, before the snow starts falling next month, to confront the reality of life on campus. I’m bringing some handlenses, my macro camera, and an endoscopic camera for poking into holes, and we’ll take a look at life in the desert of the campus lawns and shrubbery (there is some, but it’s mostly springtails, ants, and spiders). We’ll also talk about how “spider” is misleading, because there are at least 30 different species of spiders living here, alongside the human monoculture.

I’m encouraging the students to sign up for iNaturalist and to use Seek to begin their careers as natural historians. It’ll be fun! Especially since otherwise I’d be lecturing them on meiosis. You’re welcome to join in if you’re in the neighborhood of Morris, Minnesota — this is going to be casual and geared to the first year college student.