Pretty babies

I may be becoming notorious in Morris. Since we got mentioned in the local paper, I’ve gotten a few phone calls from community members asking about spiders. The latest was an excited call that a swarm of baby spiders had hatched out on their screen door…so of course we had to leap into the Spider-Mobile and race across town. I suggested to Mary that we ought to get a giant fiberglass spider mounted on the roof and one of those magnetic sirens/flashing lights that I could attach on the roof for these moments when I get emergency Spider-Alerts.

Anyway, we got there, and they were adorable. Hundreds of baby spiderlings stretching their limbs on the door.

We took a sample, but left most alone. We took a few photos and then turned them loose on a bush outside my office window. I don’t mind seeding my yard with orb weavers.

We truly are in a dark dystopian timeline

I was kind of horrified at the idea of Quentin Tarantino making an R-rated Star Trek movie — it kind of misses the point.

Star Trek is about hope. It’s about exploration and finding the right way to do things, not the easy way. It tells us how we can be better, how we too can find peace among the stars. That thematic line doesn’t seem to line up with any of Tarantino’s previous work, so unless he proves me seriously wrong, this film won’t necessarily capture the spirit of what makes Star Trek so good. It’ll just be The Hateful Eight but in space.

Now, though, something even more incongruous: they’re making a Banana Splits movie. You may remember this if you’re above a certain age, a Saturday morning live-action kids series with goofy people in goofy costumes and goofy plots which wasn’t very good, but nowadays, Hollywood is so desperate for ideas that they’re remaking any old dreck from fifty years ago.

Only to make it “fresh”, they’re remaking it as a horror movie.

I didn’t watch it when I was 12, I’m not going to watch the splatter-movie version when I’m 62.

Hey, you know what else is wrong with this timeline? David Bowie is dead, and Donald Trump is president.

Read your Bible, Ken

Here’s a beautiful fossil from the Green River beds, a whole school of fish fossilized in formation.

The article mentions that scientists are uncertain how the animals were locked down in sediments quickly enough to preserve their relative position…or even if this is behavior frozen in time, but maybe an alignment generated by whatever process imbedded them in sediments. It’s something scientists do all the time, admitting that they don’t know something.

Ah, but here comes Ken Ham, professional fool with a sense of absolute certainty. He knows the answer!

A recent article reported on the attempt by several experts to discover how this fossil, found in the Green River Formation, was formed (and I encourage you to go to the article and see the photo—it’s a truly incredible fossil!). One expert, who has studied other fossils from the Green River Formation, said that the school of fish probably died together because of a volcanic eruption, a mass of oxygen-poor water, or a temperature shift, and then all the fish fell to the bottom of the lake and were aligned by the current and then fossilized. But mathematical models appear to rule out this explanation. Others have suggested maybe a collapsed sand dune buried them, but they admitted “they don’t have a great explanation.”

But I do! Since I start with the history in God’s Word, I have the proper lens with which to view the world. This school of fish was catastrophically buried by water-borne sediments during the immediate aftermath of the global flood of Noah’s day. It’s no great mystery!

You can almost hear him giggling at the thought that he is so much smarter than those stupid scientists.

Only one problem: this stupid scientist has read his Bible, specifically, Genesis 7:11-12. His answer doesn’t work.

In the six hundredth year of Noah’s life, in the second month, the seventeenth day of the month, the same day were all the fountains of the great deep broken up, and the windows of heaven were opened.
And the rain was upon the earth forty days and forty nights.

“Catastrophic” is a somewhat ambiguous word. To trap a school of fish in situ would require an event that locked them in place in a fraction of a second. The Biblical account of the catastrophe does not propose that everything was killed and flash-frozen in a picosecond, or a millisecond, or a tenth of a second, but an ongoing disaster that dragged on for a global flood taking forty days and forty nights and leaving everything under water for a year. In Answers in Genesis’ own Creation “Museum”, they have a video recreation showing a gigantic wall of water, a tsunami rising up hundreds of feet, sweeping in and destroying a village (and killing all the happy innocent children playing in it, by the way).

A tsunami would not leave a school of fish unjumbled, just as it would not leave the corpse of a child unbattered.

I am sorry, Mr Ham, but your flood, if we postulate that it even happened, was a prolonged, violent event of unimaginable magnitude. Your own site describes it as a year-long global catastrophe that destroyed the pre-Flood world, reshaped the continents, buried billions of creatures, and laid down the rock layers. Yet when it’s convenient, you now claim that it was a delicate, swift event that froze animals in motion. It reshapes continents, but it leaves a few fish unperturbed.

I think you need to go back and read your Bible. The Book of Genesis is short, the flood is described in only a few vague pages, I’m sure that if you concentrate real hard, you can get through it all. There aren’t even any long words!

Now I know for sure that Jordan Peterson is delusional

Jordan Peterson has a brilliant idea. Not this one…

He’s pushing a new forum idea, only it’s not so new.

Jordan Peterson, the Canadian academic whom I think I could absolutely describe as a “Dingus Supreme,” has a new idea for an online platform. This is very important to Peterson because he and his largely alt-right fan base need a safe space online to share controversial opinions and practice free thought. So Peterson is launching Thinkspot, self-described as “a collaborative community where individuals can explore and exchange ideas in a thoughtful and respectful manner. The platform is an intellectual playground for censorship-free discourse.” It will also shadowban users.

The grand idea of Thinkspot, as far as I can tell, is that it’s a place for people who know how to be racist and sexist in a more dog-whistle-y way, not in the more direct way you might see on Twitter — or on Gab, the platform for people who are somehow too racist for Twitter.

I have so many questions! Here’s one. How will he coax “thoughtful and respectful” ideas from his existing fanbase of alt-right fanboys?

On his podcast this week, speaking with guest Joe Rogan, Peterson outlined how he planned to keep Thinkspot from spiraling out of control: a minimum word count. “If minimum comment length is 50 words, you’re gonna have to put a little thought into it,” Peterson said, as recapped by the right-wing site NewsBusters. “Even if you’re being a troll, you’ll be a quasi-witty troll.” I’m maybe a little more skeptical that Peterson and Rogan’s crowd — the one that spends hours at a time watching men yell into a microphone on YouTube — will have trouble coming up with 50 words to fill space.

Um, the cliche is “brevity is the soul of wit”. Long-windedness won’t help, although I am not surprised that Peterson thinks rambling on and on is the same as erudition. Also, you know that the regulars will evolve ways of turning empty noise into repetitive phrases to lengthen their comments to the appropriate length. This place is going to be the domain of droning bores practicing their mansplaining.

Here’s another scheme he has “invented”.

Even weirder was Peterson’s reveal that the site will hide downvoted comments. “If your ratio of upvotes to downvotes falls below 50-50, then your comments will be hidden. People will still be able to see them if they click, but you’ll disappear,” he said. What Peterson described is a completely valid form of site moderation. The tactic is also what conservatives have often misconstrued as “shadowbanning.”

You mean like Reddit and Disqus? All this is going to do is reinforce the majority view. Actual dissenting voices will be swiftly downvoted into oblivion. It sounds like a formula for building the most sanctimonious and stupefyingly maundering heap of trollery ever. It’s going to be a goldmine for ridicule.

I have another question.

Who pays for it? Who profits from it?

Those questions remain unanswered.

Actually, I fail to see a single thing in this paper that would require any textbook rewriting at all

Something about this title, “Evolutionary discovery to rewrite textbooks”, put me on edge. It’s a common trope to announce that your specific discovery is going to revolutionize everything, therefore you deserve more attention and glory and grant money. (Creationists seem not to understand this dynamic, though — they think scientists stick with the safe, and they think wrong, theory for all the money, when everyone knows a good, robust insight that changes minds is where the glory lies).

It’s in phys.org, though, which is generally a garbage fire of badly butchered summaries of papers, so that fact alone primes me to think the summary writer didn’t really understand the paper.

But then, it quotes the study author.

“This technology has been used only for the last few years, but it’s helped us finally address an age-old question, discovering something completely contrary to what anyone had ever proposed.”

“We’re taking a core theory of evolutionary biology and turning it on its head,” she said.

“Now we have an opportunity to re-imagine the steps that gave rise to the first animals, the underlying rules that turned single cells into multicellular animal life.”

Professor Degnan said he hoped the revelation would help us understand our own condition and our understanding of our own stem cells and cancer.

Aaaargh, no. They’re claiming that multicellular animals did not evolve from a single-celled ancestor resembling a choanoflagellate, a small protist with a single, prominent flagellar “propellor”, which many scientists consider to resemble one of the cells of sponges, called choanocytes. The idea is that the first multicellular animal would have arisen from colonies of choanoflagellates ganged together, with specialization of other cell types evolving later.

It’s fine and interesting that these investigators are proposing an alternative model, but this is not a “core theory of evolutionary biology”. It’s a likely hypothesis for the origin of a lineage of organisms we selfishly consider important, because it includes us, but it doesn’t actually revolutionize any part of the theory of evolution. Way too many scientists fail to grasp that there are the theories of evolution, that explain general mechanisms of the process, and that there are a multitude of facts of evolution, which are the instances in history that led to the specific distribution of evolutionary outcomes.

It’s like how there are physics theories that explain general phenomena: your car operates on all kinds of rules about force and acceleration and combustion. If you one day discover a shortcut on your commute to work, it may be an important personal discovery, but you don’t get to crow triumphantly about turning a core theory of automotive engineering and mechanics on its head.

But then, this is phys.org…I guess I’d better read the original paper.

It really is an interesting paper. It looks at the transcriptome of different cell types in sponges and compares them to the transcriptome of a choanoflagellate, and is basically addressing the reliability of a conclusion drawn from an observed phenotype, versus a conclusion drawn from patterns of gene expression. It’s going to argue that gene expression ought to be more fundamental, and I can sort of agree (while also seeing some problems of interpretation), but it then leaps to evolutionary conclusions from cell types, which I don’t find persuasive at all.

To summarize briefly: there are roughly three cell types in a sponge: 1) the choanocytes, which are flagellar motors that drive water flow through the animal; 2) pinacocytes, which form epithelial sheets that line the outside and insides; and 3) archaeocytes, which are found in a gooey mesenchymal smear between the layers of pinacocytes. A sponge is kind of sandwich, where the pinacocytes form the bread, the archaeocytes are the jelly, and the choanocytes are…damn, my analogy is breaking down. The choanocytes are imbedded in the bread and stir the surroundings.

The question then is, what genes are being expressed in these three cell types? And the answer is, well, lots of genes, and many of them are being differentially expressed — that is, there are genes unique to each cell type that reflect their general role.

We find that archaeocytes significantly upregulate genes involved in the control of cell proliferation, transcription and translation, consistent with their function as pluripotent stem cells. By contrast, choanocyte and pinacocyte transcriptomes are enriched for suites of genes that are involved in cell adhesion, signalling and polarity, consistent with their role as epithelial cells.

Now though, they raise an evolutionary question. They identify all these genes, and then ask which are common to single celled eukaryotes, which are common to multicellular animals, and which are unique to sponges. This gives a rough estimate of the evolutionary age of these genes; the first category is the oldest, found in pre-metazoan organisms, the second category may have arisen at the approximate time of origin of the metazoan lineage, and the third category would have appeared later as the sponge lineage specialized. They determined the relative contributions of these three categories to the patterns of gene expression in the three cell types.

The A. queenslandica [the sponge species] genome comprises 28% pre-metazoan, 26% metazoan and 46% sponge-specific protein-coding genes. We find that 43% of genes significantly upregulated in choanocytes are sponge-specific, which is similar to the proportion of the entire genome that is sponge-specific. By contrast, 62% of genes significantly upregulated in the pluripotent archaeocytes belong to the evolutionarily oldest pre-metazoan category, significantly higher than the 28% of genes for the entire genome. As with archaeocytes, pinacocytes express significantly more pre-metazoan and fewer sponge-specific genes than would be expected from the whole-genome profile.

Does this diagram help interpret that?

a, Phylostratigraphic estimate of the evolutionary age of coding genes in the A. queenslandica genome. b–d, Estimate of gene age of differentially expressed genes in choanocytes (b, top), archaeocytes (c, top) and pinacocytes (d, top) and the enrichment of phylostrata relative to the whole genome (b–d, bottom). Asterisks indicate significant difference (two-sided Fisher’s exact test P <0.001) from the whole genome. The enrichment values (log-odds ratio) for: choanocytes (b; n = 10) are sponge-specific (−0.0089, P = 0.7747), metazoan (–0.0361, P = 0.9958) and premetazoan (0.0439, P = 0.0004) genes; archaeocytes (c; n = 15) are sponge-specific (−0.5634, P = 1.33 × 10−133), metazoan (−0.1923, P = 1.04 × 10−18) and premetazoan (0.6772, P = 0); and pinacocytes (d; n = 6) are sponge-specific (−0.2173, P = 5.23 × 10−13), metazoan (−0.0008, P = 0.5231) and premetazoan (0.2359, P = 3.07 × 10−36).

OK, maybe not. Shorter summary: archaeocytes express lots of old genes, which makes sense, given we already had it explained that they’re enriched for genes involved in control of cell proliferation, transcription and translation, which are also ancient, primitive functions. Pinacocytes are also doing fairly basic things, and like the archaeocytes, are switching on basic essential genes. The choanocytes, though, are exceptional, and are turning on lots of sponge-specific genes that evolved after sponges diverged from other metazoans. The conclusion: choanocytes are switching on derived spongey genes that evolved for a spongey lifestyle, while archaeocytes are more generic, switching on a universal toolkit for adaptable stem cells, which have to be able to change their roles to become any of the three cell types.

They also make the point that the choanoflagellate gene expression pattern is most similar to that of the archaeocytes. From these observations, they argue that the ancestral metazoan more resembled a stem cell, like an archaeocyte, than a choanoflagellate.

…we posit that the ancestral metazoan cell type had the capacity to exist in and transition between multiple cell states in a manner similar to modern transdifferentiating and stem cells. Recent analyses of unicellular holozoan genomes support this proposition, with some of the genomic foundations of pluripotency being established deep in a unicellular past. Genomic innovations unique to metazoans—including the origin and expansion of key signalling pathway and transcription factor families, and regulatory DNA and RNA classes—may have conferred the ability of this ancestral pluripotent cell to evolve a regulatory system whereby it could co-exist in multiple states of differentiation, giving rise to the first multicellular animal.

And that’s where they lose me. I don’t buy their interpretation.

First, organisms do not evolve by descent from cell types. The whole genome is passed down. That choanocytes express a certain subset of genes is irrelevant — they carry the whole suite of genes, as do the pinacocytes and archaeocytes. You wouldn’t do a gene expression profile of human brain cells and compare it to the profile for mesenchymal cells, and then argue that brain cells are weird and unique, therefore we didn’t evolve from brain cells. Of course we didn’t! Your assumptions make no sense.

Second, what they found was that choanoflagellates exhibit a broader, more general pattern of gene expression than sponge choanocytes. This makes sense. Sponges are truly multicellular, with specialized subsets of cells that carry out specific roles, while choanoflagellates are unicellular, where each cell has to be a jack-of-all-trades. Yes, a choanoflagellate is going to have to use all of its genes, while individual cells in the sponge have the luxury of focusing on a smaller set of jobs. Choanocytes are specialized, they’re going to have a different expression profile than a generalist cell.

Third, choanoflagellates have an expression profile similar to an archaeocyte…but this is not in contradiction to their phenotype of having a flagellar collar. The metazoan ancestor could still have been a choanocyte, and nothing in this evidence contradicts that possibility!

All they’re really saying when you get right down to it is that metazoan ancestor had to have the capacity to generate diverse cell types later in its evolution, which is kind of obvious. They’re also arguing that the ancestral metazoan could not have been as locked in and limited in its repertoire of functions as a choanocyte in an extant sponge, which, again, is a given. What is not obvious is that the ancestor had to have been archaeocyte-like in form and function.

I also get the impression that the authors have been soaking in the transcriptomics literature and practice to the extent that they’ve lost sight of the bigger picture. They’d only have an argument if descendant forms were derived from the RNA of their ancestors…which actually would revolutionize the theory of evolution! Fortunately, they are not making that claim at all.

Sogabe S, Hatleberg WL, Kocot KM, Say TE, Stoupin D, Roper KE, Fernandez-Valverde SL, Degnan SM & Degnan BM (2019) Pluripotency and the origin of animal multicellularity. Nature https://doi.org/10.1038/s41586-019-1290-4

Is there something funny going on at Patheos?

I was contacted by someone who said there are simmering complaints in the comments sections at Patheos — some are seeing heavy-handed filtering, in particular, that comments discussing Beliefnet or Patheos itself are getting blocked. You can see some of those concerns expressed in comments to this post by Ed Brayton. I don’t comment on that network, so I haven’t seen it myself.

Interestingly, there is a precursor to this concern from 2017. Several Patheos bloggers jumped ship back then, concerned that the religious conservatives who owned the network were meddling with the content.

Yvonne Aburrow, one of the writers who left Patheos, summed up the feelings of some of the writers: “If there are to be blog aggregators or multi-blog hosting sites, they need to be independently-owned, collective, and egalitarian. I (and many others) are just not comfortable with the corporate world being able to control our content, especially if that corporate world is too closely linked with the evangelical Christian right.”

Huh. Interesting. We recently killed the advertising on Freethoughtblogs (which was managed by Patheos!) because it was pathologically annoying and getting in the way of our ability to just write, at the expense of all of our revenue…yeah, we’re writing for you for free right now. I guess we’re living the dream of Ms Aburrow, but it also means we put a damper on any expansion plans for a while.

It’s been a fecund kind of day

We spent the afternoon largely engaged in moving our Parasteatoda females into larger, roomier quarters, using 5.7L Sterilyte containers, and then cutting up cardboard boxes to make frames inside the containers for them to build on. We discovered that the 10-can mini-can pop cases were exactly the right size to fit inside, so we zipped over to the grocery store and purchased way too many cases, just so we could get the cardboard. I bought most of it for my research student, who requested Mountain Dew — he’s sharing the bounty with his roommates, so it will be all my fault if a swarm of college students wired on caffeine rampage through the town tonight.

Yesterday, Mary and I went to Pomme de Terre Park, and has been our custom, prowled around looking for spiders. We found a magnificent Larinioides living in a tin shed down by the river, and caught it and brought it home. Look at it! It’s huge and beautiful!
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