I am inclined to like this hypothesis

I’m still going to criticize it, though.

For years, anthropologists and evolutionary biologists have struggled to explain the existence of menopause, a life stage that humans do not share with our primate relatives. Why would it be beneficial for females to stop being able to have children with decades still left to live?

According to a study published today in the journal Proceedings of the Royal Society B, the answer is grandmothers. “Grandmothering was the initial step toward making us who we are,” says senior author Kristen Hawkes, an anthropologist at the University of Utah. In 1997 Hawkes proposed the “grandmother hypothesis,” a theory that explains menopause by citing the under-appreciated evolutionary value of grandmothering. Hawkes says that grandmothering helped us to develop “a whole array of social capacities that are then the foundation for the evolution of other distinctly human traits, including pair bonding, bigger brains, learning new skills and our tendency for cooperation.”

I guess I’m personally inclined to appreciate the importance of grandmothers, having had a pair of good ones myself, and seeing how much time my wife invests in our granddaughter, but I’m less impressed with the study, which is based entirely on a computer simulation. I don’t trust simulations of complex phenomenon that necessarily have to simplify all the parameters. What about aunts and sisters? What about uncles?

What about the grandfathers?

None of those individuals are of interest, because this version of the hypothesis is structured around explaining menopause as the product of selection. Nope, I don’t buy it.

But why would females evolve to only ovulate for 40 or so years into these longer lives? Hawkes and other advocates of the hypothesis note that, without menopause, older women would simply continue to mother children, instead of acting as grandmothers. All children would still be entirely dependent on their mothers for survival, so once older mothers died, many young offspring would likely die too. From an evolutionary perspective, it makes more sense for older females to increase the group’s overall offspring survival rate instead of spending more energy on producing their own.

I’m willing to accept the benefit of an extended family and social cooperation, but the effort to justify menopause seems misplaced. There are many grandmothers who are not menopausal, and there would have been even more in ancient populations, where pregnancy shortly after the onset of menstruation would have been common. It also doesn’t explain the contributions of sisters and aunts to childrearing, or that brothers and sisters, who are also “distractions” from the business of raising a single delicate child. Why couldn’t it benefit a woman to raise her own child born late and also contribute to the well-being of grandchildren born to previous offspring? I suspect the simulation has assumptions built into the code about how much grandparental investment can be offered if they also have a child.

But, yeah, what about the grandfathers?

We help, too. So why isn’t there a male menopause where our testicles shrivel up and make us more willing to contribute to child-rearing? A man has a certain number of progeny, then boom, the reproductive urge goes away and he has to sit down and focus on taking care of the kids he’s got. Or his grandchildren. Or his nieces and nephews. That would be the logical endpoint of this arch-selectionist model, after all, and what’s good for the goose is good for the gander.

Yet somehow people feel compelled to come up with adaptationist explanations for accidents of evolutionary history.

Did native Americans have more equality 9000 years ago than we do now?

A pretty picture of a Peruvian hunter from 9000 years ago, bringing down vicuna with her atlatl and spear:

The image is based on the remains of the dead hunter, and an analysis of grave goods.

At Wilamaya Patjxa, an archaeological site in southern Peru, archaeologists unearthed the skeleton of a young woman whose people buried her with a hunters’ toolkit, including projectile points. The find prompted University of California Davis archaeologist Randall Haas and his colleagues to take a closer look at other Pleistocene and early Holocene hunters from around the Americas.

Their results may suggest that female hunters weren’t as rare as we thought. And that, in turn, reminds us that gender roles haven’t always been the same in every culture.

“The objects that accompany [people] in death tend to be those that accompanied them in life,” Haas and his colleagues wrote. And when one young woman died 9,000 years ago in what is now southern Peru, her people buried her with at least six stone spear tips of a type used in hunting large prey like deer and vicuña (a relative of the alpaca). The points seem to have been bundled along with a stone knife, sharp stone flakes, scraping tools, and ocher for tanning hides.

I also learned a new genetics fact! The bones were fragmentary, and the bits that you use for a morphological assessment of sex had crumbled to dust. But you can sex a skeleton by looking at the proteins that make up tooth enamel.

Tooth enamel contains proteins called amelogenins, which play a role in forming the enamel in the first place. The genes that produce these proteins are located on the X and Y chromosomes, and each version is slightly different. As a result, people who are genetically female have slightly different amelogenins than people who are genetically male. The proteins in the ancient hunter’s tooth enamel had a distinctly female signature, with no trace of the Y chromosome version.

The hunter from Wilamaya Patjxa is a young woman with the tools of an activity usually associated with men. If the objects people are buried with are the objects they used in life, then that raises some questions.

Maybe she was some weird outlier, I hear you ask. So they surveyed what was found at other grave sites, and it looks like a significant fraction of ancient hunters in the Western hemisphere happened to be women.

The hunter from Wilamaya Patjxa raises a similar question: was she the exception that proved the rule, or does her burial suggest that (in at least some ancient cultures) women were sometimes hunters? To help answer that question, Haas and his colleagues looked for other ancient people who had been buried with hunting tools. In published papers from archaeological sites across the Americas, they found 27 people at 18 different sites: 16 men and 11 women.

…the fact that so many apparent women turned up on that list is surprising. “Female participation in early big-game hunting was likely nontrivial,” wrote Haas and his colleagues. They suggest that as many as a third to half of women across the ancient Americas may have been actively involved in hunting.

The final line in this article is perfect.

Based on animal bones at Wilamaya Patjxa, large game like vicuña and taruca (a relative of deer) were extremely important to the community’s survival. In that case, hunting may have been an all-hands-on-deck activity. Haas and his colleagues also suggest that letting other members of a community keep an eye on the kids while the parents hunted might have freed more women up to bring home the bacon—or venison, in this case.

In other words, whether women hunted or fought probably depended on social factors, not biological ones.

I thought I ought to let David Futrelle know about this, since it makes the title of his blog even more ironic, but he beat me to it and has already posted about how She Hunted the Mammoth.

Crunchies vs. Squishies: ask the pterosaurs

I’m not a taxonomist; early in my career I settled on the model systems approach, which meant all the nuances of systematics disappeared for me. “That’s a zebrafish” and “that’s not a zebrafish” were all the distinctions I had to make, and zebrafish were non-native and highly inbred so I didn’t have to think much about subtle variations. There was one taxonomic boundary one of my instructors forced me to recognize: Graham Hoyle had nothing but contempt for “squishies”, as he called vertebrates like fish or mice or people, and was much more focused on the “crunchies”, insects and crustaceans and molluscs. These seemed like odd ad hoc taxonomic categories to me, I and could think of lots of exceptions where “crunchies” were pretty squishy (see witchetty grubs or slugs), and “squishies” were armored and crunchy (armadillos, any one?), and besides, as a developmental biologist, they were all squishy if you caught them young enough. But OK, if you like dividing everything into two and only two categories, go ahead.

Then today I read this paper, “Dietary diversity and evolution of the earliest flying vertebrates revealed by dental microwear texture analysis”, and saw that there was at least one practical use for the distinction. What you eat affects wear patterns on your teeth, that if you eat lots of crunchy things vs. lots of squishy gooey things, you’ll have a different pattern of dental scratches, and since teeth fossilize — unlike guts — you can get an idea of what long dead animals had for dinner. Furthermore, you can compare fossil microwear textures to the textures in extant animals, where you do know what kinds of things they eat.

This is cool — so you can estimate the range of things ancient pterosaurs ate from how their teeth were worn, whether they ate lots of soft-bodied bugs like flies, or hard-shelled crustaceans, or soft-fleshed fish, by making a fine-grained inspection of their fossilized teeth and comparing them to modern reptiles.

a–c Reptile dietary guilds; a piscivore (Gavialis gangeticus; gharial), b ‘harder’ invertebrate consumer (Crocodylus acutus; American crocodile) and c omnivore (Varanus olivaceus; Grey’s monitor lizard). d–f Pterosaurs; d Istiodactylus, e Coloborhynchus (PCA number 5) and f Austriadactylus (PCA number 2). Measured areas 146 × 110 µm in size. Topographic scale in micrometres. Skull diagrams of extant reptiles and pterosaurs not to scale.

But they’re not done! Knowing the phylogenetic relationships of those pterosaurs, you can then infer evolutionary trajectories, getting an idea of how dietary preferences in species of pterosaurs shifted over time.

a Phylo-texture-dietary space of pterosaur microwear from projecting a time-calibrated, pruned tree from Lü et al.33 onto the first two PC axes of the extant reptile texture-dietary space. b Ancestral character-state reconstruction of pterosaur dietary evolution from mapping pterosaur PC 1 values onto a time-calibrated, pruned tree from Lü et al.33. To account for ontogenetic changes in diet, only the largest specimen of respective pterosaur taxa, identified by lower jaw length, were included. Pterosaur symbols same as Fig. 2. Skull diagrams of well-preserved pterosaurs not to scale (see ‘Methods’ for sources).

These results provide quantitative evidence that pterosaurs initially evolved as invertebrate consumers before expanding into piscivorous and carnivorous niches. The causes of this shift towards vertebrate-dominated diets require further investigation, but might reflect ecological interactions with other taxa that radiated through the Mesozoic. Specifically, competition with birds, which first appeared in the Upper Jurassic and diversified in the Lower Cretaceous, has been invoked to explain the decline of small-bodied pterosaurs, but this hypothesis is controversial. DMTA provides an opportunity for testing hypotheses of competitive interaction upon which resolution of this ongoing debate will depend.

In summary, our analyses provide quantitative evidence of pterosaur diets, revealing that dietary preferences ranged across consumption of invertebrates, carnivory and piscivory. This has allowed us to explicitly constrain diets for some pterosaurs, enabling more precise characterisations of pterosaurs’ roles within Mesozoic food webs and providing insight into pterosaur niche partitioning and life-histories. Our study sets a benchmark for robust interpretation of extinct reptile diets through DMTA of non-occlusal tooth surfaces and highlights the potential of the approach to enhance our understanding of ancient ecosystems.

So pterosaurs started as small bug-eaters and diversified into niches where they were consuming bigger, more diverse prey over time, which certainly sounds like a reasonable path. I don’t know that you can really assume this was a product of competition with birds — I’d want to see more info about the distribution of pterosaur species’ sizes, because expanding the morphological range doesn’t necessarily mean that you’re losing at one end of that range, but I’ll always welcome more ideas about how Mesozoic animals interacted.

Tell me again how evolutionary psychology is not a con game

This is how evo psych works: state your hypothesis about past human societies with absolute confidence in the absence of any evidence, and then follow up with how The Lord of the Rings supports your model of a transition from a brutish form to a more gracile, effeminate form. Geoffrey Miller demonstrates:

So, the kill count competition between Legolas and Gimli is easily understood evidence of the evolution of warfare. Does that make Aragorn a transitional form?

When will the criticisms of evolutionary psychology sink in?

I’ve been complaining for years, as have others. The defenders of evolutionary psychology just carry on, doing more and more garbage science built on ignorance of evolutionary biology, publishing the same ol’ crap to pollute the scientific literature. It’s embarrassing.

Now Subrena Smith tries valiantly to penetrate their crania. It’s a familiar explanation. She sees it as a matching problem between their claims about the structure of the brain and behavioral history.

The architecture of the modern mind might resemble that of early humans without this architecture having being selected for and genetically transmitted through the generations. Evolutionary psychological claims, therefore, fail unless practitioners can show that mental structures underpinning present-day behaviors are structures that evolved in prehistory for the performance of adaptive tasks that it is still their function to perform. This is the matching problem.

In a little more detail…

Ancestral and present-day psychological structures have to match in the way that is needed for evolutionary psychological inferences to succeed. For this, three conditions must be met. First, determine that the function of some contemporary mechanism is the one that an ancestral mechanism was selected for performing. Next, determine that the contemporary mechanism has the same function as the ancestral one because of its being descended from the ancestral mechanism. Finally, determine which ancestral mechanisms are related to which contemporary ones in this way.

It’s not sufficient to assume that the required identities are obvious. They need to be demonstrated. Solving the matching problem requires knowing about the psychological architecture of our prehistoric ancestors. But it is difficult to see how this knowledge can possibly be acquired. We do not, and very probably cannot, know much about the prehistoric human mind. Some evolutionary psychologists dispute this. They argue that although we do not have access to these individuals’ minds, we can “read off” ancestral mechanisms from the adaptive challenges that they faced. For example, because predator-evasion was an adaptive challenge, natural selection must have installed a predator-evasion mechanism. This inferential strategy works only if all mental structures are adaptations, if adaptationist explanations are difficult to come by, and if adaptations are easily characterized. There is no reason to assume that all mental structures are adaptations, just as there is no reason to assume that all traits are adaptations. We also know that adaptationist hypotheses are easy to come by. And finally, there is the problem of how to characterize traits. Any adaptive problem characterized in a coarse-grained way (for example, “predator evasion”) can equally be characterized as an aggregate of finer-grained problems. And these can, in turn, be characterized as an aggregate for even finer-grained problems. This introduces indeterminacy and arbitrariness into how adaptive challenges are to be characterized, and therefore, what mental structures are hypothesized to be responses to those challenges. This difficulty raises an additional obstacle for resolving the matching problem. If there is no fact of the matter about how psychological mechanisms are to be individuated, then there is no fact of the matter about how they are to be matched.

One problem is that evolutionary psychologists all seem to think that their assumptions are obvious — and if you don’t agree, why, you must truly hate Charles Darwin and be little better than a creationist. Man, it’s weird when the intelligent design creationists are all calling you a dogmatic Darwinist, and the evolutionary psychologists are accusing you of being an intelligent design creationist. They’re both wrong.

Everyone likes cute furries more than spiders, I’ve noticed

I can’t be the only one who reads outside my discipline to get material to help me cover all those evolutionary phenomena I know little about. I know a bit about fish and arthropods, but my understanding of the details of mammalian evolution is a bit thin — yet for some reason, students are more interested in the history of mammals than of spiders. I really appreciate it when I stumble across information that fills in the gaps in my knowledge in presentable ways, and Nature has done just that with a graphically rich article on How the earliest mammals thrived alongside dinosaurs. There is lots of good stuff here, and I particularly like the emphasis on the importance of fossilized infants. Development matters!

Sometimes it goes a little too far, though — for example, this illustration is way too dense to be useful, but it it interesting.

That is not a spider

Grrr. The CBC got me excited with a headline about “the granddaddy of spiders”. It’s not a spider. It’s a Cambrian chelicerate, which ought to be cool news enough without pretending it’s some kind of familiar organism. At least it wasn’t SciTech, which called it a frightening 500-million year old predator” or LiveScience, which called it a “nightmare creature”. C’mon, people. It was a couple of centimeters long. I do not like this pop sci nonsense that has to jack up the significance of a discovery by pretending it was scary. Does this look scary to you?

a–c, Reconstructions. a, Lateral view. b, Dorsal view (the gut has been removed for clarity). c, Isolated trunk exopod. an, anus; lam, lamellae.

At least the article by the discoverers is sensible. This is an early Cambrian chelicerate with those big old feeding appendages at the front of the head (which spiders also have) and with modified limb appendages that resemble book lungs (also a spider trait), but they are most definitely not spiders. They are their own beautiful clade, and cousins of Mollisonia plenovenatrix might have been spider ancestors, but calling them spiders is like excavating an ancient fish and calling it a mammal. Very misleading.

Yes, I’m being pedantic. It matters. Let’s not diminish the diverse chelicerates by calling them spider wanna-bes.

Here’s the abstract for the paper.

The chelicerates are a ubiquitous and speciose group of animals that has a considerable ecological effect on modern terrestrial ecosystems—notably as predators of insects and also, for instance, as decomposers. The fossil record shows that chelicerates diversified early in the marine ecosystems of the Palaeozoic era, by at least the Ordovician period. However, the timing of chelicerate origins and the type of body plan that characterized the earliest members of this group have remained controversial. Although megacheirans have previously been interpreted as chelicerate-like, and habeliidans (including Sanctacaris) have been suggested to belong to their immediate stem lineage, evidence for the specialized feeding appendages (chelicerae) that are diagnostic of the chelicerates has been lacking. Here we use exceptionally well-preserved and abundant fossil material from the middle Cambrian Burgess Shale (Marble Canyon, British Columbia, Canada) to show that Mollisonia plenovenatrix sp. nov. possessed robust but short chelicerae that were placed very anteriorly, between the eyes. This suggests that chelicerae evolved a specialized feeding function early on, possibly as a modification of short antennules. The head also encompasses a pair of large compound eyes, followed by three pairs of long, uniramous walking legs and three pairs of stout, gnathobasic masticatory appendages; this configuration links habeliidans with euchelicerates (‘true’ chelicerates, excluding the sea spiders). The trunk ends in a four-segmented pygidium and bears eleven pairs of identical limbs, each of which is composed of three broad lamellate exopod flaps, and endopods are either reduced or absent. These overlapping exopod flaps resemble euchelicerate book gills, although they lack the diagnostic operculum. In addition, the eyes of M. plenovenatrix were innervated by three optic neuropils, which strengthens the view that a complex malacostracan-like visual system might have been plesiomorphic for all crown euarthropods. These fossils thus show that chelicerates arose alongside mandibulates as benthic micropredators, at the heart of the Cambrian explosion.

I think this diagram illustrates the relationship of M. plenoventrix to spiders well.

a, Simplified consensus tree of a Bayesian analysis of panarthropod relationships. This tree is based on a matrix of 100 taxa and 267 characters. Extant taxa are in blue; dashed branches represent questionable groupings. Asterisk shows that the radiodontans resolved as paraphyletic. This analysis excludes pycnogonids, but this had little effect on the topology. The letters A to D at the basal panchelicerate nodes refer to boxes on the right, and summarize the appearances of major morpho-anatomical features: (1) extension of cephalic shield, including a seventh tergite; (2) cephalic limbs all co-opted for raptorial and masticatory functions, and reduction of some trunk endopods; (3) dissociation of the exopod from the main limb branch; (4) presence of chelicerae; (5) trunk exopods made of several overlapping lobes; (6) some cephalic limbs differentiated as uniramous walking legs; (7) multi-lobate exopod covered by sclerite (operculum); (8) reduction of seventh cephalic appendage pair; and (9) all post-frontal cephalic limb pairs are uniramous walking legs. b, Life reconstruction. Drawing by J. Liang, copyright Royal Ontario Museum

Not a spider, but still cute and adorable.

Aria C, Caron J-B (2019) A middle Cambrian arthropod with chelicerae and proto-book gills. Nature https://doi.org/10.1038/s41586-019-1525-4.

I don’t understand it, therefore nobody does

We’re going to see a wave of ignorance prompted by David Gelernter’s profession of foolishness, aren’t we? Every fool in the world who hears that guy’s nonsense is now inspired to spew out some nonsense of their own.

One example is Barbara Kay, who I’ve never heard of before, pontificating in the National Post that “there’s one mystery we still can’t explain”. Only one? I can think of lots. But the fact that there are still questions in the world does not mean that all the answers we have are wrong.

Her point is especially bad, because she singles out one thing that she thinks is false, and she is wrong about it.

The human brain and the power of speech put humans way beyond the boundaries of Darwin’s own three critical criteria for natural selection, which; i) may expand an animal’s power only to a point where it has survival advantage — and no further; ii) cannot produce changes that are “injurious” to the animal; and iii) cannot produce a “specially developed organ” that is useless to an animal at the time it develops. If a Neanderthal brain three times the size of any primate’s and a unique capacity for speech do not constitute “specially developed organs,” what does?

OK. Start with Darwin: he’s not our infallible prophet. He got a lot wrong, and remember, he was writing 150 years ago. You can demonstrate Darwin’s errors all you want, and modern scientists will just shrug and say, “So?”

Kay’s second error, though, is that she overlooked the meaning of her subject, natural selection. Evolution is not synonymous with natural selection, and showing that something could not have evolved by natural selection does not refute the idea that it evolved by some other mechanism. Even if we take those three points as given, it does not negate the idea of evolution.

Third error: she has not demonstrated that point (i) means natural selection could not have occurred. Where does the survival advantage of speech stop? It seems to me that the initiation of speech with grunts and crude vocalizations could only be improved, and improved continuously, by natural selection. Speech that enabled better hunting could lead to speech that is used for love poetry, or describing geography, or telling scary stories around the campfire, or expressing philosophical thoughts. She has not demonstrated any barrier which would impede the action of natural selection.

Fourth error: The brain isn’t that special (ii). All animals have one (well, we could call sponges and jellyfish exceptions). Our ancestors had one that could visualize the environment and the future, allow for sophisticated socialization, and permitted all kinds of communication shy of speech. Speech capability builds on structures that are already present in a multitude of animals.

Fifth error: brains that could process information in a complex way before speech evolved were not useless to our ancestors (iii), even if they couldn’t speak.

Sixth and biggest, most common error in creationists: the failure of their imaginations and ignorance of the evidence does not support their claim that the science is wrong. I can’t imagine how Barbara Kay manages to type words on a machine, but I think it’s clear that she did. Probably. I can’t rule out the possibility that an editor filtered the output of a monkey pounding on a keyboard, but it’s more likely that her essay was produced by a human being who simply knows nothing about biology.

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

Teams of Memes, bursting from the seams

Image courtesy of the googles.

Daniel Dennett’s From Bacteria to Bach and Back is a lengthy and winding journey. It is characterized (including by its publisher) as a general explanation of the evolution of minds and various peculiar mental functions, consciousness and language being the two most hotly discussed by philosophers, but there’s a better way to read it. As its best, the book is a tour of Dennett’s personal philosophical repertoire, illustrating how ideas from his books and papers fit together.

Dennett’s general theory of the development of genetics stems from his broad theory of memes, where a meme is any informational entity that can be transmitted and replicated. The rough idea is that minds are meme-machines in the way that organisms are gene-machines (in Dawkins’ analogy of the gene’s-eye-view). This is a fruitful analogy, in some respects, though I think it can and should draw some skepticism from readers. I’ll return to those worries later.

The basic building blocks of Dennett’s view are indicated by gestures and short explanations, which is a challenge since he’s spent so much time discussing and arguing for them elsewhere in his work. In any case, there are really two that it is important to understand.

[Read more…]