What good is a lab without water?

That is my sad face. I went into the lab yesterday to get a bunch of things done, when I learned that the water to the whole building was shut off. Our science building is only about 20 years, but every year we have a battery of problems that shake out — rooms are too hot or too cold, the roof leaks, and come the winter, we often get pipes freezing and all the problems that causes. So no water for three days while the maintenance crew fixes everything.

This would have been catastrophic when I was working with fish, and it’s still awkward when working with spiders. On my list was the need to set up more flies so they’d have food in two weeks, washing spider poop out of their containers, and most tragic of all, I had set hundreds of vials soaking in soapy water the day before, and I was going to scrub ’em up and rinse them out and dry them yesterday.

Look! I even got a brand new bottle brush! I was so excited to be doing dishes, and then…crashing disappointment. I’ll have to wait until Thursday.

A New Year’s Spider

I was inspired by this essay by Amal El-Mohtar, who is building a tradition of finding A New Year’s Bird. I like it, it seems like a lovely way to start the year, but I’m not much of a bird person — that’s my wife’s thing. By the way, Mary is right next to me, staring out the window at the visitors to our bird feeders as part of her participation in FeederWatch. But you know me, I’m more of a spider person. Sorry. Not sorry.

It was clear, though, that I need a New Year’s Spider. I began my quest.

One easy possibility was that, this morning, as I showered and reached into the soap dish, I startled a small cellar spider, which scurried frantically away. I girded myself with my camera and walked the few feet to our bathroom to search for the little fellow.

I failed. It was not there any longer. That was OK, though, because that is how all quests must begin, with failure and frustration, and we then find redemption through struggle. I will find the beast.

The bathroom had to be explored. The lights above the bathtub are separated by a grid, a hot spot for spider webs, and there was plenty of spoor. The space was dusty and full of cobwebs, and I searched everywhere, finding diaphanous fluff everywhere, but not a hint of the spider. They are cunning and cautious, and are good at finding small cracks in the walls and hiding in the space between the drywall and siding, inaccessible to giants like me.

Where must I go? There’s no doubt. At some point in a quest, we must descend into the underworld. Our basement, that is — a dark, cold place, neglected and unfrequented by people, where we never dust or clean, where spider-kind can flourish. But again, this is mid-winter, and even spiders struggle when the cold obliterates their prey, and survival is a matter of patience and stillness and long waiting. I lit a torch, opened the creaking, little-used door, and descended the narrow stairs into the cavern.

The space is mostly empty, containing a few dusty relics from a time when it was inhabited by boisterous teenagers, but now barren of anything that might attract a human visitation, except, in my case, billowing cobwebs. Those cobwebs were all empty of life, unfortunately. Not even spiders find this basement an oasis in the depths of winter — too cool, too empty of food, too gloomy. I searched the main room and found a few traces of previous occupation, mainly molted skeletons lying about like the carcasses of facehuggers. Where are they now, I wondered? What victims were drained of blood after they shed their cuticle?

Further. I went deeper, and found the basement ogre: a large sheet web, a meter across, with scraps of cuticle scattered about, and imbedded in the area the skeletons of large prey, houseflies and bumblebees, that had stumbled into this cursed place and found their doom. There was movement on the sheet! I briefly glimpsed a large funnel weaver, horrified by the bright light I’d brought into their domain. It immediately scuttled back into it’s lair, refusing to face me. I could not count this as my New Year’s Spider. I needed a bold creature that would face me, stare into my eyes, and not retreat like a coward. There was no honor in this spider.

Deeper still, I went into the small twisty rooms in the back, where the furnace burned. What I immediately found was…death. The spiders had retreated into the faint warmth as cold seeped into the underworld, finding final refuge where the hot heart of the house dwelt, and many had died in the process. So many spider corpses! So many large carcasses dead in their webs, on the wall, on the ceiling.

I knew I was close. How else would a quest go? First the barren land, then the monster in the dark, then death, then finally, the grail and revelation. There she was, queen of the dark world, my New Year’s Spider, resting on the underside of a shelf, gazing unafraid and unmoving at me.
Returning to the land of light, I can now rest with a sense of accomplishment, perhaps ready for a new year. As one who has returned, I can now give you a quest, to find your own New Year’s Spider.

Or bird, I guess, if you prefer.

(I know way too many people here are Bird Persons who don’t much care for spiders, so I only posted the text here, with none of the photos of horrifying spider webs, dead spiders, and the Queen of Darkness. You could see all the grisly photos if you’re subscribed to my Patreon, or you can see the spider queen on Instagram.)

“It’s on her left foot!”

The health minister in Queensland, Australia was interrupted when a huntsman was found crawling on her.

Wait, wait, she’s talking about the impact of COVID-19 on her community — the spider is cute and adorable (although we don’t even get a photo of it), but isn’t that a relatively unimportant part of the event to be making the news? If I were there, I’d volunteer to cuddle the spider so she can get on with the important message.

Stop it, Australia, I’m a married man!

That continent keeps trying to seduce me, and it just isn’t right. Look, they’re finding new species of jumping spiders all the time. Those hussies, and their dancing.

And then they’re publishing temptations. It’s spider porn. How am I supposed to resist?

I can’t afford to fly to Australia, so maybe I’ll just have to get a copy of that field guide so I can flip through it in idle moments, you know, to read the articles.

My hip hop band name will be “RTA Clade”

Now my brain is stuck on spider evolution, which is an awesomely cool subject, and how annoyed I am that creationists can spit on it with such ignorant contempt. So I have to mention another good article on the subject, Reconstructing web evolution and spider diversification in the molecular era. There are so many papers on this topic, and there’s a guy affiliated with the Discovery Institute writing a whole book on the subject while unforgivably ignorant of it all. So here, cogitate on this:

Optimization of web architecture on the preferred topology. Black stars indicate strong support for a node from both MP (jackknife > 75%) and Bayesian (posterior probabilities > 90%) analyses, and gray stars indicate nodes strongly supported only by one methodology or with jackknife 50–74%. Branch colors represent MP reconstruction of webs, and pie charts represent the relative probabilities from ML reconstructions. Colors of boxes to the left of taxon names represent their webs, and open boxes indicate that taxa do not spin prey capture webs.

There’s also information on the topic of orb web monophyly that I mentioned in the previous post.

The monophyletic origin of orb webs is strongly supported, despite conspicuous differences in the silk used to spin different types of orbs. This has important implications for understanding both web evolution and spider diversification. Instead of cribellate and ecribellate orb webs evolving in parallel, orb monophyly explicitly implies that dry cribellate capture spirals were replaced by ecribellate gluey spirals. This involves 2 major changes. First, a shift in the silk used to produce the core fibers of capture threads, resulting in novel tensile properties. The core fibers of modern (ecribellate) orb weavers are composed of flagelliform silk, which is much more elastic than the pseudoflagelliform silk core fibers of cribellate spiders. Mechanically, flagelliform silk functions like rubber, relying on entropy to resist motion of silk molecules and absorb kinetic energy during prey capture, allowing the capture spiral to expand and contract repeatedly. In contrast, cribellate silk relies on permanent rupturing of molecular bonds to absorb kinetic energy and deforms irreversibly during prey capture. The second major shift involves the mechanism of adhesion, from dry cribellate fibrils that adhere through van der Waals forces and hygroscopic interactions to chemically adhesive viscid glue in ecribellate spiders. This results in webs with greater adhesion per surface area and may have facilitated the transition from horizontal to vertical web orientation in modern orb spiders, which is associated with increased prey interception rates.

That paper also discusses something I didn’t mention. Did you know that about half of all spider species don’t make prey capture webs at all? They’re active hunters, like wolf spiders and jumping spiders, and they belong to an extremely successful monophyletic group called the RTA clade, short for retrolateral tibial apophysis, the best band name ever.

I think I need to go spend some time in the lab with my spiders to cool my brain down, before participating in the podcast this afternoon, which will not be about spiders.

This cannot be tolerated: creationists lying about spider evolution

Oh dear. Oh dear oh dear oh dear. The Discovery Institute has turned it’s puerile, feeble attention to spiders now, and it’s as pathetic as you might imagine. It’s written by a guy, Eric Cassell, who felt it important to mention that he had an undergraduate biology degree, which he earned at least four decades ago, before committing to work in — take a wild guess — engineering, of course. Much as I respect many engineers and their work, it sure tends to breed inappropriate teleological attitudes in the brains of its practitioners.

This article, The Miracle of Spiderwebs, is typical of the type. First, talk about how freakin’ complicated spider webs are, then declare that they don’t understand how they could have evolved, which therefore means it could not have evolved. Never mind that spiders have been dependent on silk for their survival for 350 million years and there has been constant selection for more effective functionality, some old guy with negligible background in biology can’t understand it! Furthermore, it can’t possibly be because he’s an ignorant ass, he has to misrepresent the current science to make his case.

Despite great effort, humans have yet to produce anything functionally equivalent to silk. Through genetic engineering, attempts have been made to duplicate it without success. The main challenge is replicating the sophisticated and information-rich protein molecules found in the silk produced by spiders and other silk-producing arthropods such as silkworms — proteins that are nearly double the size of average human proteins. Smaller proteins do not have the strength or flexibility of spider silk. Given the advanced genetic and manufacturing technologies available today, it is remarkable that spider silk still cannot be duplicated. This illustrates just how advanced the engineering design of spider silk is.

No, he’s wrong. The silk molecules tend to be long, but not particularly “information-rich”, whatever that means. They are made up of long stretches of highly repetitive amino acid sequences, interspersed with special purpose regions. The strength comes from the repetition — they fold into crystalline bricks made of beta-pleated sheets. The length of each molecule is an obstacle to synthesizing them, of course, but there’s nothing magical or incomprehensible about the genes.

Rather, what makes them difficult to replicate is the silk production apparatus. The silk gland stores a large quantity of the fluid suspension of the silk molecules, but to make a silk fiber requires passage through a long duct that physically compresses and stretches the fibers as it extracts water and acidifies the environment, causing a controlled phase transition that makes the silk molecules align and precipitate to build a continuous fiber. That’s the hard part. It’s the gene (relatively easy) plus the specific mechanical and chemical processing that makes the silk. It is not at all remarkable that we can’t duplicate that process, but there’s nothing divine about it.

But that’s all there is to this article. Gosh, it’s amazing what biology can accomplish, says the guy who thinks it’s all about engineering.

Various spiderwebs, even among spiders of the same species, are far from identical. The most obvious reason for the differences is that each is tailored to its specific location. As the Goulds explain, “Every set of initial anchor points is different; the number of radii is contingent on opportunity; the beginning of the sticky spiral depends on where the longest several radii turn out to be. In short, each web is a custom production.” The Goulds postulate that spiders have a form of mapping ability that enables them to implement general design principles in a wide variety of circumstances. This is demonstrated, for instance, by spiders successfully making repairs to damaged webs.

And…? So…? The reason every web is a custom production is that nature is not uniform. A spider has an algorithm for navigating a variable environment: an orb weaver lays down radial lines from a central point to convenient anchor points, then walks a spiral, laying down sticky threads. The process builds a recognizable, functional sheet that varies depending on structures in the neighborhood. What is the miracle here?

Providing credible evolutionary explanations for the origin of silk and web design has proven problematic. Several theories have been proposed for the origin of both, but none have been generally accepted. Biologist and spider specialist William Shear concedes that “a functional explanation for the origins of silk and the spinning habit may be impossible to achieve.” One complicating factor is that the webs of some spiders that are more distantly related are nearly identical. Shear writes, “It appears probable that several web types are the product of convergent evolution — that is, that the same web has evolved in unrelated species that have adapted to similar environmental circumstances.” But as I will argue in Chapter 6, that is an unconvincing explanation for the origin of complex programmed behaviors.

For someone cited by a creationist, WA Shear sure has a lot of publications on the paleontology and evolution of spiders and other invertebrates. It looks like his work might have been mined to extract a misleading quote, and yep, he sure has.

That brief quote is taken from an article titled, “Untangling the evolution of the web,” and surprise, surprise, surprise, the creationist has left out the bulk of the context. I know, a creationist lies about the scientific literature? Say it ain’t so! But here’s the full and accurate quote from the paper. It starts, “A functional explanation for the origins of silk and the spinning habit may be impossible to achieve”, but then there’s a goddamn COMMA.

A functional explanation for the origins of silk and the spinning habit may be impossible to achieve, but the evolution of silk-spinning organs has been studied, and debated, extensively. Revealing evidence has come from the histology of silk glands — the details of their cellular construction — and from the embryological development of the spinnerets themselves. Histological evidence allows us to draw connections, or homologies, between silk glands in different spider groups, and embryology shows clearly that the spinnerets are paired abdominal appendages, with the silk issuing from modified setae, or hairs. So much information is available on the anatomy of the spinning apparatus, in fact, that the traditional view of web evolution rests heavily on a classification derived from the form and position of spinnerets.

This is one of those things about the creationist literature that makes me thoroughly furious: they unethically misrepresent and actively distort the work published in the credible scientific literature to pretend they are scholars. They aren’t. They’re liars. And they spin their lies out into collections of self-reinforcing nonsense. I note that the creationist here seems to think that convergent evolution is somehow an unacceptable explanation for the origin of multiple kinds of webs, and cites his own goddamn book, authored by a creationist engineer with no qualifications at all in this field, and ignores the fact that his source, WA Shear, goes on to give a summary of the evolution of diverse webs. That’s not a book worth reading, obviously.

Also, that Shear article contains a simple, clear illustration of the pattern of evolution that this creationist twit thinks can’t exist.

Phylogenetic tree shows how some families of spiders may have arrived at similar and different web designs. The Mesothelae are generally believed to have evolved first from the common ancestor of all spiders, followed by the Mygalomorphae and the “true spiders”, the Araneomorphae. The monophyletic hypothesis of orb-web origin (which is incorporated into this diagram) holds that the orb-web was invented by an araneomorph, the common ancestor of araneoid and uloborid spiders, that had a cribellum. The cribellum was acquired by a spider that was the common ancestor of all araneomorphs, including the araneoid superfamily and the uloborids. The araneoids lost the cribellum, and some araneoid families later lost the orb. Among the uloborids and their close relatives, the dinopids, are many species that have modified the orb.

But wait! There’s much more, all conveniently left out of Cassell’s stupid mangling of the article. We do have good models for the evolution of spider webs, all based on, as Shear notes, the evidence from taxonomy and histology and molecular biology.

Hypothetical pathways of spider-web evolution form a tangled web of their own, with the question of the orb’s origin, and its role as a possible precursor to other webs, at the center. In several cases it’s not clear which web is ancestral; it is possible that some aerial sheet webs preceded the orb web, whereas others developed from the orb. Pathways that are less likely are indicated by light-orange arrows; for some of them there is no direct evidence.

Oh look. Someone had the proper respect for the evidence and was happy to talk about the strengths and weakness of the support for their model, and it wasn’t Eric Cassel.

I’ll also note that Cassel is relying on a generalist article from 1994 which incorporates little of the evidence from modern molecular phylogenies. He didn’t understand the 27 year old article, there’s little hope he could grasp a modern analysis, in which the details of evolution have been strengthened. Here’s an example from 2012, Early Events in the Evolution of Spider Silk Genes:

Spidroin gene tree is based on a ML analysis of the carboxy-terminal encoding region with gaps coded as binary characters and monophyly of some groups constrained (see Methods). Numbers next to nodes and terminals correspond to numbers in supplementary Tables S1 and S2 showing support values, alternate rootings, and continuous character data. Spidroins are colored according to the taxonomic group from which they were characterized: purple = Mesothelae, blue = Mygalomorphae, green = Araneomorphae. Gray squares indicate duplication events inferred by reconciliation. Hash marks on branch indicate arbitrary shortening of branch for figure quality purposes. Brackets indicate clades with the following abbreviations: AcSp = Aciniform, TuSp = Tubuliform, PySp = Pyriform, MaSp = Major ampullate, MiSp = Minor ampullate, Flag = Flagelliform.

A more fundamental challenge for those seeking to provide a detailed, causally credible explanation for the origin of silk and spiderweb architecture is the number of genes involved in producing silk, and the complex genomes of spiders. After decades of failed attempts to provide a causally adequate explanation, one can be forgiven for concluding that we have no compelling reason to assume that a step-by-step evolutionary pathway to such an information-rich substrate actually exists. And as we will discuss later, there are now some positive reasons to consider that such information-rich systems have for their source something other than a purely blind material process. Here, suffice it to say that the behaviors and functions associated with both silk and web spinning exhibit many characteristics of human engineering, and engineering of a very high order.

Repeat after me:

Complexity is not evidence of design.

Complexity is not evidence of design.

Complexity is not evidence of design.

Also repeat after me:

My ignorance is not evidence of design.

My ignorance is not evidence of design.

My ignorance is not evidence of design.

Biologists have provided causally adequate explanations for the origin and evolution of diverse spider webs, Mr Cassell is simply intentionally and maliciously ignoring them, and further, lying about the content of the scientific literature to make a claim that arachnologists are as ignorant as he is. He’s also logically contradictory.

If, Given the advanced genetic and manufacturing technologies available today, it is remarkable that spider silk still cannot be duplicated, how can you then turn around say that webs exhibit many characteristics of human engineering, and engineering of a very high order?

This is an odd video to go “viral”

I don’t get it. It’s a half-minute long video of a black widow hanging from a bit of silk, twirling about randomly (it’s below the fold if you want to see it). It’s a pretty animal, but the behavior is strange. I’ve never seen my related theridiidae do this. They’re either in repose, waiting for their next meal, or moving efficiently and purposefully to, for instance, add to their cobweb, or attack some prey, or scurry to a safe corner. Just dangling from a single thread, that’s weird, and makes me wonder about the context. Is she sick? Has she been traumatized?

If that’s all it takes to go viral, I clearly need to get into the lab and make videos of spiders doing interesting things.

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