An hour of mathematical genetics homework

We Americans have all had a pleasant Thanksgiving and possibly an indulgent Black Friday, but it’s time to get back to work. Yesterday, Zach Hancock gave a presentation on why the hereditarian fallacy is a fallacy — the math doesn’t work. The video demonstrates an important truth: biology requires math. In this case, it’s a fairly simple level of math, so if you know a little algebra and maybe a little statistics, you should be able to cope.

It’s an important message, too. Racism and hereditarianism are built on a false premise, and anyone who tries to use population genetics to argue against evolution or for racism doesn’t understand some rather basic stuff.

It gets in some good digs against Steven Pinker, too, who clearly doesn’t understand genetics or basic math.

Now get to work. Your break is over.

Another step in the evolution of multicellularity

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

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

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

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

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

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

Much better. The key points are:

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

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

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

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

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

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

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

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

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

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

Another fun computer game you can play!

If you don’t care about birds flitting about, here’s another tool, TimeTree. It’ll let you look up the divergence time between any two species, in this case I just chose to compare myself with my house spiders.

700 million years sounds about right, but that’s just the general time since the last common ancestor of vertebrates and invertebrates. Our shared ancestor would have been some nondescript little worm.

If you’re arguing with Kent Hovind, it might be useful to know that the last common ancestor of humans and bananas lived about 1.5 billion years ago; same time since we diverged from the amoeba. The paleo-proterozoic was a busy time! Or, at least the seas were full of eukaryotes then.

Crabby destiny

This diagram from Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments is going to reinforce the idea that everything converges on crabs…which is kind of cool anyway.

Summary of phylogeny and divergence time estimates for Brachyura (88 brachyuran families, 263 genera, 333 species, 338 individuals plus 6 outgroups). Posterior ages were estimated in BEAST2 using a fixed topology resulting from the concatenated ML analysis in IQ-TREE, 36 vetted node calibrations, a birth–death tree prior, and relaxed lognormal clock model. Shaded circles at nodes represent ultrafast bootstraps. Pie slices are colored by superfamily, with the outermost ring colored by taxonomic section. Line drawings, one representative per superfamily (numbers corresponding to taxa in Supplementary Table S7), by Javier Luque and Harrison Mancke.

Please note, this diagram illustrates the evolution of a single, large, successful clade, the Brachyura. It does not imply that humans and salamanders and spiders are going to converge on a crablike form, OK? The interesting thing is that all the descendants of this Triassic lineage, despite going through multiple independent transitions from marine to terrestrial and back again, have assumed these very similar (superficially, at least) forms, and that tells us something interesting. The Brachyura have some internal constraints that shape their evolution, and studying them help us understand the balance between inherited patterns and external forces. That’s the conclusion of the paper, that there are constraints on evolution.

Herein, we inferred a large molecular phylogeny of true crabs, estimated divergence times that were older than previously thought, and estimated the number of transitions from marine to non-marine lifestyles. We found up to 17 convergent transitions through direct and indirect pathways, with at least 3 climbing to higher degrees of terrestrial adaptation. The most highly terrestrial clades were some of the oldest non-marine inferences in our data, with their common ancestors having diverged over 66 Ma. At least 9 more recent events throughout the Cenozoic led to crabs living in intertidal and marginal marine environments, a shift that is estimated to be much easier based on lower threshold liability and likely fewer traits required. As instances of convergent evolution provide emerging models in the form of “natural experiments,” the framework we have developed to compare the gradient of adaptations will enable future research that aims to “predict” the constraints leading to repeated trait evolution and better understand the drivers of biodiversity across related groups.

Evolution destroyed in 5 minutes!

I can’t believe how embarrassed I am for Eric Hovind and John Harris. Eric is, of course, the son of Kent Hovind, which is humiliation enough, and John is the director of Living Waters Europe, so you’d think being shackled to that doofus Ray Comfort would make you reluctant to appear in public, but no, they now appear together in a video that has them capering ludicrously and giggling like maniacs because, oh boy, they’ve got those evolutionists now. They have a knock-’em-dead argument against evolution (it’s always against evolution, because they lack a defensible alternative) that will finally finish off evolution, and it’s so simple they can present it in 5 minutes. Except they don’t. This is a 40 minute video.

Discover “How to Destroy Evolution in 5 Minutes.” Using the lens of mathematics to critically examine the evolutionary timelines from chimp DNA to human DNA renders Evolution, once again, IMPOSSIBLE!

This compelling argument has left evolutionists speechless as they watch their evolutionary science foundation implode.

Join Eric Hovind and John Harris, Director of Living Waters Europe, for an insightful look at one of the most compelling arguments against evolution you will ever hear!

I’m sure they do leave many people speechless. I know I was stunned when I heard it, because it was so appallingly stupid and grossly overhyped. You can skip the first 30 minutes of the video, because it’s just John and Eric patting each other on the back, bragging about how sciencey they are, and rehashing bits of biology 101 (“this is what DNA looks like…”) that are completely irrelevant to their argument, and boasting about how they’ve left people completely convinced that they’ve destroyed science and are now going to church. It’s extremely obnoxious, especially when you get to their actual argument, which is abysmally unimpressive.

It’s Haldane’s Dilemma. It goes in cycles, where very few years some creationist rediscovers this idea, and goes raving looney claiming that they’ve disproven evolution, and then slowly goes quiet as evolutionary biologists look at them funny and then ignore them. It was first brought up by JBS Haldane in 1957. Haldane was a great scientist, not a creationist, and he brought it up as a potential problem in population genetics that needs to be resolved. It was the problem of substitutional load, that for a mutation to go to fixation involved a cost to the population, since replacement of one allele by another involved the virtual death of members of that population over time. So how could we possibly get enough mutations to transform a chimp-like animal into a person, since surely there are a vast number of genetic changes between the two? Haldane didn’t know how many, but must be lots, right?

Very smart people — much smarter than John & Eric, who know nothing about biology or evolution — wrestled with this problem, but the real question was not whether evolution could occur, but where was the error in Haldane’s assumptions or calculations. As molecular biology proceeded onward, undaunted by a theoretical problem, it was discovered that populations were hugely polymorphic, that is, contained a huge reservoir of widespread variation, that was incompatible with Haldane’s Dilemma. Either the premises for the math was wrong, or plants and animals existed in defiance of the natural laws of the universe.

Evolutionary biologists quickly figured out the flaw. Most of that variation is neutral and can accumulate with little cost. Gosh, empirical reality overcomes the theory, especially the relatively primitive theory of the 1950s. Creationists did not get the memo, though, and every few years they bring up Haldane’s calculations as if they were an evolution-stopper, rather than an early step in figuring out the dynamics of population genetics.

You can skip the whole video, though. It’s only appeal is the spectacle of watching two bozos engaged in a 40-minute pratfall. Here’s their ultimate evolution-killing calculation, presented at about the 30 minute mark.

Note that they are bending over backwards to use numbers that will favor evolution, which is why so much of this calculation is nonsense. Humans and chimps differ by 1% of their genome (it’s more like 3%, but OK), which means there are about 30 million base pairs that differ (they neglect the fact that these are two independently evolving lineages so each needs 15 million changes…let’s forget that, since their numbers throughout are so silly.) That means that in 10 million years at the rate of 1 beneficial mutation (an absurd number) every 20 years, the population can accumulate at most 500,000 beneficial mutations. But we need 30 million! Oh noes!

Every lay person will be baffled by the numbers and will be confused. Every evolutionary biologist will look at it in shock and wonder why this idiot is roaming the streets unsupervised.

You won’t be taken aback. You’ll note that the assumption of 30 million (or 100 million, or whatever) beneficial mutations is false, since most of the differences are neutral or nearly so, so we can just throw away the whole estimate. You might also comment on the fact that their formula is very linear, assuming that evolution is a long march forward, steadily adding beneficial mutations progressively to produce us humans, rather than a process of constantly branching diversification. You’ll also acknowledge that sexual recombination allows genes to evolve in parallel and be reshuffled into novel arrangements. Their little demo disproves creationist evolution, which is an entirely different process than biological evolution.

There’s little point in engaging with anyone presenting this level of ignorance and misinformation. Just pat them on the head, give them a lollipop, and encourage them to stay in school.

There are limits to how much creationists can deny

Here’s a headline for you: H5N1 virus in latest human case has mutated, officials say. This is not a surprise. This is the lesson we are thoroughly familiar with in biology, that everything changes over time. Of course H5N1 is evolving.

Testing of the latest human case of bird flu has revealed a “notable” mutation in the virus, officials have said.

The case, which was identified this month in a dairy worker in Michigan, marks the second human infection linked to the multi-state H5N1 outbreak among US cattle.

Genomic sequencing has now found a change in the virus compared to an earlier infection in a dairy worker in Texas, raising concerns that the virus is evolving to better infect humans.

The slight change in the virus’s genetic makeup is “associated with viral adaptation to mammalian hosts,” the Centre for Disease Control said in a statement published on Friday.

Mutation and adaptation are inevitable. We ought to be teaching that with a heck of a lot more confidence, because some people don’t get it. Answers in Genesis is in the business of spreading doubt and confusion, and they have their own stupid opinions about bird flu.

However, many media outlets and health authorities have expressed the fear that the virus could “mutate” to a form which is capable of directly spreading among humans. The 1918–19 “Spanish flu” outbreak, which swept the world and killed more than 20 million people (more even than the just finished war, and than the Black Death in 14th century Europe), is believed to have possibly started in birds and spread to humans.

They are very fond of scare quotes.

Unfortunately, the words being used to describe the feared change in the virus, such as “mutate” and “evolve” carry with them all sorts of Darwinian baggage. This will become especially pointed if the dreaded change does eventuate. Viruses, like actual living things, do mutate (the term is properly applied) and change. The issue is, as always, not to be misled by the “psychological link” between such terms and the idea that pond scum has turned into pelicans, palm trees and politicians.

Eventually, even the ignorant turdlets at AiG are compelled to admit that organisms actually do mutate, and change, and adapt, they have to desperately insist that that does not mean that viruses will evolve into human beings. Yeah, we know. No one has predicted that they would. You can use as many quotes as you want, but you’re still forced to admit that life “mutates” and “adapts” and “evolves.”

Evolution is a real and ongoing process, and that’s why we should be concerned about H5N1.

A Carboniferous arachnid

This week has been a good one for chelicerate evolution. Here’s another fossil, Douglassarachne acanthopoda, which was creeping around in the forests of Illinois in the late Carboniferous.

Douglassarachne acanthopoda n. gen. n. sp., holotype and only known specimen FMNH PE 91366; for interpretative drawings and scale, see Figure 2. (1) Part, detail of distal femur and more-distal podomeres, showing nature of curved macrospines on lateral edge of distal podomeres, bases of macrospines on dorsal surface of femur; (2) counterpart, detail of posterior opisthosoma showing bilobed structure at base of anal tubercle.

What is it? I don’t know. The authors are unsure. It’s an arachnid, but it could be in the spider lineage or the harvestman lineage, or it could be its own weird thing. It’s spiderish, anyway.

Douglassarachne acanthopoda n. gen. n. sp., reconstruction of the possible appearance of the animal in life.

An Ordovician ancestor to spiders

On this Memorial Day, I’m going to have to have a discussion with my spiders about their distinguished, noble ancestry. It was kind of Nature to publish a study of their many-times-great grand uncles, an ancient euchelicerate named Setapedites abundantis, a common fossil found in Moroccan sediments that are about 478 million years old, which puts it right in the middle of the Great Ordovician Biodiversification Event, a key moment in the evolution of modern taxa.

This is not a spider, though. It belongs in the euchelicerata, the large systematic group that includes spiders, scorpions, ticks, horseshoe crabs, sea scorpions, and other extinct groups. As you might guess from the name, a key feature is the presence of chelicerae, anterior appendages that in spiders carry the venomous fangs. It also has a common feature we see in both spiders and horseshoe crabs, the fusion of the anterior segments to form a prosoma, with posterior segments forming the abdomen or opisthosoma.

While it’s a cool looking little dude, it’s marine and pretty remote from modern chelicerates. From the dorsal side, it looks like an undistinguished little crustacean, of a type that was probably swarming in Ordovician seas.

A, B MGL.102899 and interpretative drawing, articulated specimen in dorsal view. C, D MGL.102828 and interpretative drawing, articulated specimen in dorsal view. E, F MGL. 102872 and interpretative drawing, articulated specimen in dorsal view. Abbreviations: btg, bipartite tergites; mr, median ridge; pl, pleura; pr, prosomal rim; saxn, sub-axial node; sr, sunken region; t1–11, tergites 1–11; t, telson; tk, telson keel. Scale bars, (A–F) 1 mm.

Where it gets interesting is when it’s flipped over, and you get a glimpse of the mass of limbs.

A, B YPM IP 517932c and interpretative drawing (counterpart), articulated specimen in ventral view. C, D YPM IP 517932c and interpretative drawing, chelicerae, and labrum anatomy detail. E, F Close-up of the prosoma of MGL.102934 and interpretative drawing, in dorso-lateral view. G, H Close-up of the prosoma of MGL.102634 and interpretative drawing, in ventral view. I, J Close-up of the prosoma of MGL.102800a under alcohol and polarized lighting, and interpretative drawing, in ventral view. Abbreviations: 1–6, podomeres 1–6 of the exopod; ptp, pretelsonic process; bs, basipodite; bst, brush-like setae; che, chelate podomere; db, doublure; lb, labrum; ss, single setae; st, pair of setae. Chelicerae are highlighted in gray, endopods in blue, exopods in green, opisthosomal appendages in red, and the pretelsonic process in purple. Scale bars, (A, B) 1 mm; (C, D) 100 µm; (E–K) 500 µm.

In front of the jaws proper (labrum, lb) it has a pair of small chelicerae (che). These have since evolved into the massive, sharptoothed chompers you can see my tarantula using to turn a mealworm into macerated mush.

Setapedites wasn’t such a fierce predator. Here’s what it looked like.

Illustration by Elissa Sorojsrisom.

Cute, right? I don’t know why it’s drawn as a swimmer, though — with that anatomy, it looks more like a benthic organism.

The final bit of interesting information is that they mapped out the correspondences in the segmentation of this animal with other, similar fossils and the extant Xiphosurians.

Simplified extended majority rule tree of a Bayesian analysis chronogram of euchelicerate relationships, based on a matrix of 39 taxa and 114 discrete characters, showing the position of Setapedites abundantis within Offacolidae. Lineages extending after the Silurian are indicated with arrowheads. Schematic models of the body organization in Habelia, Setapedites abundantis, Dibasterium, Offacolus, and Xiphosurida illustrate the origin and early evolution of euchelicerate uniramous prosomal appendages and tagmosis. Roman numbers designate somites. Prosoma somites are highlighted in blue, pre-abdomen somites in yellow, abdomen somites in brown, and the possible anal pouch or post-ventral structure (pvs) in purple. Black dorsal lines indicate tergites and cephalotorax. Schematic model of Xiphosurida Offacolus, and Dibasterium from 45, Habelia

Also of note: Setapedites had biramous appendages, a feature that is mostly kind of lost in modern arthropods — the outer branch got adapted into gills and lungs and even wings.

I can’t help but notice that domestication and artificial selection turns wolves in little yapping Pomeranians, but natural selection turns shrimp into tarantulas.