The journey begins — I’m off to the @AAS_arachnology meetings

It takes a while to escape the gravitational pull of Morris, Minnesota, so we’re about to leave for the Twin Cities so I can catch an early morning flight to exotic Lexington, VA for the American Arachnological Society 2019 meeting. It feels a bit strange. There’s some imposter syndrome going on in my head, only I really am an imposter — I just started exploring arachnology this year, so I’m nothing but a novice.

I’m going to pretend I’m a bewildered and confused and uncertain first-year graduate student at this meeting. Just ignore the wrinkles and the grey beard, OK?

I’m also excited to get my first spider meeting t-shirt.

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.

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, 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…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

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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New spider housing!

I got some excellent suggestions from Nicholas DiRienzo for raising spiders, which is why it’s good to get information online, and also why I’m going to the American Arachnology Society conference this weekend. You can get started with reading stuff, but there’s no substitute for hearing it straight from the experts.

We checked out the couples we’d put together in larger spaces yesterday, and sadly, I caught one in the act of cannibalism…poor guy. We separated them. Then I rummaged in my collection of zebrafish containers, and found some 5.7L Sterilyte containers, a bit smaller than Dr DiRienzo recommended, but we’ll give them a try. We moved a few females into them right away so they can start getting used to the expanded digs. We’re going to also add some cardboard liners, once we find a box that fits.

I was initially daunted about the space required — it was appealing to just have oodles of spiders in a small incubator — but once I started stacking these things, I realized I could pack maybe as many as 50 females into the space I’d previously used for my zebrafish setup. Sorry, fishies, it’s now an arachnid facility.

My summer student, Preston Fifarek, has wisely chosen to name the female spiders after characters from Game of Thrones. Males are going to get Lord of the Rings names. I’ll be interested to see how well Cersei takes to Bilbo.

My day is all booked up already

I have plans, so many plans.

First, I’m going into the lab to examine yesterday’s handiwork. We attempted to breed two pairs of spiders yesterday, moving them into two different kinds of larger chambers. My concern is that the vials we keep them in are too small for two spiders and that one of the reasons I’m seeing so much cannibalism of the males is because of overcrowding. If all goes well, I’ll find two females and two live males today. If that works, I’m going to turn my incubator into a fornucopia and pair up all the males with mates. I’d like, for a change, to have more embryos than I know what to do with.

Then we’re surveying some more garages. I’ve arbitrarily set a one week window for data collection in June, so that will be done tomorrow.

This afternoon I have to transcribe all the data into my computer — right now I’ve got a pile of folders and scribblings on paper for each site. I’m keeping paper records of everything (hey, election officials — it’s a good idea!), but I’ve got to get it organized in one place so I can wrap my head around it.

One of the things I have to sort out is some of the bigger picture data. I’m being scrupulous about data privacy — every site is encoded on a master list, and then the individual site data is stored without direct reference to the homeowners (which is good, I planned ahead thinking people might not want it known how many spiders occupy their property), but now I’m seeing glimmerings of interesting spatial distributions of species. I might want to make a map at some point.

In some ways, the data so far is kind of boring. Because we restricted ourselves to one narrow kind of environment, garages and sheds, we’re seeing the same beasties everywhere: Pholcus and Steatoda and Parasteatoda. That’s good for our sanity, because we’re brand new at this spider game, so reducing the number of taxa we have to master simplifies everything. We know, though, that there are hundreds of species around here, and we only occasionally see an orb weaver or funnel web spider or ground spider in these dusty musty cobwebby garages. We might want to think about sampling other sites in the future.

For instance, houses around Lake Crystal here in town have been stunning when we walk up to knock on the front door — the houses are covered in webs, there are swarms of mosquitos and mayflies everywhere, we start out convinced that this place is going to a time-consuming nightmare to sort out. Then we walk into the garage, and dang, it’s nothing but Theridiidae and Pholcidae again, and not particularly rich in them, either. We’re focused on these sheltered mini-environments while there’s a riot going on outside. Maybe at some point, if I get a student interested in that sort of thing, we’ll just stake out an area on the lakeshore and go centimeter by centimeter through that more complex space.

Right now, though, just the relationships between these few species in our limited environment are going to take a while to puzzle out. Garages are either infested with Pholcus or Parasteatoda, but mixed distributions are less common. Will we see shifts over the summer? Do the pholcids, known predators of other spiders, gradually take over? Is there something in the environment that favors one species over another?

We’re also seeing some interesting granularity in the species distribution, which is one reason I’m thinking of mapping. We find Parasteatoda tepidariorum everywhere, it’s probably the most common spider in these sites. But then we found one house that was all S. triangularis, and two widely separated houses with lots of S. borealis. Just chance? Are there little enclaves of these species, like ethnic neighborhoods, that persist over time? If we go door-knocking and check other houses in these neighborhoods, will we find larger patterns?

I haven’t even started on the lab studies. Once we get steady production of embryos, we’re going to start with some simple studies of the effect of temperature on rate of development, seeing if we can induce diapause, that sort of thing, all with the aim of figuring out how spiders survive living in a place where temperatures drop to -20°C every winter. My summer months are split with one week of taxonomic studies to three weeks in the lab, so that’s actually going to take up more of our time soon.

I feel like I’m getting sucked down into a spider hole. It’s delightful! I recommend it! You should all join us down here!

You think spiders are weird? At least I’m not working on turkeys.

Those birds are creepy.

They began with a taxidermically prepared female turkey model and a pen of active males. In order to learn what specifically gets a turkey visually interested in making more turkeys, the two men slowly removed parts of the turkey model, one by one. They detached the feet, the wings, and eventually the entire body of the taxidermied turkey until the stick-mounted head and neck, held like the grimmest puppet, remained.

In their paper “Stimulae Eliciting Sexual Behavior” the scientists write: “Male turkeys presented a body without the head displayed but did not mount. Presenting the head alone (upright) released display behavior followed by ‘mounting’ and copulatory movements immediately posterior to the head.”

That’s a bit of evidence that bozo defending the missionary position didn’t consider. See? Turkey faces are a potent visual stimulus to other turkeys, even when decapitated and impaled on a stick.

I don’t understand how non-vegetarians can even bear to eat those things.

My house: ground zero in the Northern Empire of Spiders

We were out spider-huntin’ again today, adding more data to the collection, and finding this Steatoda, which is about as big as they get. We’ve captured a couple of representatives of this species now, but they’re all female.

We limit the number we capture to one or two a day, because we don’t want to perturb the local populations too much. I’m only planning to breed Parasteatoda tepidariorum, though, so I’m going to have to do something with the other species we find…I’m probably going to release them all at my house, since I did so much collecting here that the population is hopelessly messed up already, which may turn my house into a weird little hotbed of exotic spider diversity.

I wonder if that will increase the property value? It should.

What paleo diet?

I keep hearing about this imaginary paleolithic diet, and I wonder how they know, and also find it strange that there was apparently one people a 100,000 years ago, and they all ate the same things. Everything about it seems wrong.

Now there is some evidence that humans were roasting starchy tubers in their caves.

Based on plants that would have been locally available, Stone Age people likely cooked tubers and roots in the cave, the scientists say. Compared with raw starchy plants, their cooked counterparts would have provided an especially efficient source of glucose, and thus energy, to people. Human fossils previously found in the coastal cave, located at Africa’s southern tip, also date to around 120,000 years ago.

Ancient starch eating at Klasies River Cave supports the possibility that Homo sapiens evolved genetic upgrades to help with digesting hard-to-break-down starch long before people started farming starchy crops in Africa around 10,000 years ago. Scientists have determined that people today carry more copies of starch-digestion genes than did Stone Age populations, such as Neandertals and Denisovans.

Ancient humans in southern Africa likely ate a mix of cooked roots and tubers, shellfish, fish and game animals, Larbey’s team says. Roots and tubers would have been available year-round. And while little is known about the origins of cooking, campfires were being built at least 300,000 years ago in Africa.

Well, maybe there is something to this paleo diet stuff, because I started salivating. I don’t have any shellfish or game, but I’m thinking now that dinner tonight might be some roasted tubers seasoned with some of the herbs my wife is growing in her garden. Our many-times-great grandparents weren’t stupid people. We might as well give those starch-digestion enzymes they bestowed on us a happy workout!