Burying the dead

If you have a subscription to Netflix, you might want to watch Unknown: Cave of Bones, about the discovery of Homo naledi in the Rising Star cave system. It’s spectacular.

On the other hand, if you’re claustrophobic, you might want to skip it. I’m not particularly, but I watched the video of those women wriggling their way down a narrow crack to reach the Dinaledi Chamber gave me a rising sense of panic. There’s no way I could put myself in that position without having a screaming heebie-jeebie fit.

If you can get past that, though, it’s worth it to watch the adventure of science.

Dear god I hate this

This is terrible. All that graphics arts skill gone to waste as someone tries to illustrated something they don’t understand.

Evolution as a linear path towards a particular, narcissistic goal (of course, it’s all about us!) The implications of a teleological purpose. The self-centeredness. The trimming of diversity. Notice how everyone under genus Homo is stereotypically male — all the prior stages may have been masculine in the artist’s mind, too, but it’s hard to tell. This is going to fuel so many continued misconceptions.

At least the conclusion mentions that “Humans are still evolving,” but they should have shut up with that, rather than making predictions. Why should we all converge on a “‘Great Averaging’ where continuous, international mixing will create an average of all current physical differences”? Will drift and mutation stop? Will all population structures break down? Do chance and varied environmental pressures disappear, to favor one pattern of humans being “taller, more lightly built, and less aggressive with smaller brains”? Well, maybe the “smaller brains” is a reasonable extrapolation from our current experience.

I see the creator has “two Master of Science degrees (one in Geochemistry/Astrobiology, another in Biomedical Communications).” I can tell evolutionary biology wasn’t one of them.

It takes multiple mechanisms to drive evolution

I went through high school thinking that evolution was pretty neat. I read all the popular treatments — those Time/Life books, National Geographic, science magazines, etc. — and they made it sound like Darwin had got everything right in 1859. I could go along with that.

But then, in 1975, I went off to college and had access to a university library and started reading the real hardcore stuff. I was just mainlining PNAS & Science & Nature & Evolution & the Journal of Embryology and Experimental Morphology and soaking in all this exciting stuff, and that’s when I discovered the concept of genetic drift (specifically, thanks to Lewontin). My mind was blown. Suddenly, questions I had never even thought to ask were answered with clarity. Certainly nothing in biology makes sense except in the light of evolution, but likewise nothing in evolution makes sense except in the light of neutral genetic drift.

I guess Holly Dunsworth had the same revelation, and also noticed the sad gap in public education.

In the USA, K-12 evolution education standards are missing GENETIC DRIFT as well as the word NEUTRAL.

(see here: https://www.nextgenscience.org/topic-arrangement/hsnatural-selection-and-evolution)

I don’t know how to understand life’s perpetual change without those fundamentals.

If students know about meiosis (which *is* in the standards), then they know about genetic drift. It’s just a matter of linking meiosis to evolution.

Genetic drift is a very simple concept and makes natural selection make a whole lot more sense!

I shout about this on Twitter and I get “just be happy anyone teaches evolution in K-12 at all” and “teachers don’t know about drift” in response. But evolution without genetic drift is not evolution, and if teachers knew about drift, then they’d be more comfortable teaching evolution. I guarantee it!

Without drift, it’s too easy to just replace God with natural selection. And that habit of narrating evolution by giving agency to natural selection is super-duper weird for non-believers let alone for believers! (This a no hatred of religion, faith, or creationism zone.)

Genetic drift paves the way for thinking about and then narrating evolution as the constant change that life/nature/biology is. Everyone gets that time is just constant change and they will get that nature/biology/life is too. They embody it themselves, being different from their parents.

Plus, continuing to teach evolution as only being natural selection (which is what the standards are doing), is also dangerous. That selection-obsessed mindset is tied to racism, sexism, essentialism… all the stuff that we have to remove from our species’ shared origin story. Darwin only had selection (not drift, etc) to work with and look what his imagination did with evolution: racism, sexism, essentialism

Oh wow, yes. I’ve got to stand up and cheer at that. Also specifically the bit about meiosis, because I’m teaching genetics right now and am constantly emphasizing the role of chance in inheritance. We’re built on a platform of coin flips and die rolls and long shots in heredity, yet somehow in our public education, that all vanishes and is replaced with something close to fixed destiny (in higher ed, that isn’t true, fortunately. Usually.)

Also, drift nicely bridges all those gaps in comprehension the creationists love to inflict on us.

Fire, 250,000 years ago

The experts are now explaining that Homo naledi almost certainly used fire to explore caves & cook food. This isn’t huge surprise, because how else could they have maneuvered through the pitch black darkness of an elaborate cave system?

Last August, Berger climbed down a narrow shaft and examined two underground chambers where H. naledi fossils had been found. He noticed stalactites and thin rock sheets that had partly grown over older ceiling surfaces. Those surfaces displayed blackened, burned areas and were also dotted by what appeared to be soot particles, Berger said.

Meanwhile, expedition codirector and Wits paleoanthropologist Keneiloe Molopyane led excavations of a nearby cave chamber. There, the researchers uncovered two small fireplaces containing charred bits of wood, and burned bones of antelopes and other animals. Remains of a fireplace and nearby burned animal bones were then discovered in a more remote cave chamber where H. naledi fossils have been found.

This is where the creationists are going to have to get creative in their excuses, because many of them (including Answers in Genesis) have declared that H. naledi was just an ape. Joel Duff explains the conundrum they face.

But don’t worry, they’ll just invent some improbable impossible ridiculous bullshit to justify whatever conclusion they want.

Oh no, it’s a meme

Herbert Spencer would be so proud.

One quibble: evolution by natural selection isn’t the fundamental concept, it’s evolution, change, by multiple mechanisms.

The red button comic is also relevant.

Yeah, because it’s virtually impossible to teach a creationist anything.

A nice summary of human evolution

It’s a listicle, of course, but it’s written by an archaeologist, which is good, but she was the recipient of a Templeton grant, which triggers my skepticism. But she makes 6 points about our history:

Species such as Homo Longi have only been identified as recently as 2018. There are now 21 known species of human.

And 20 of them went extinct. We’re part of a dying tree.

Hybrid species of human, once seen by experts as science fiction, may have played a key role in our evolution. Evidence of the importance of hybrids comes from genetics. The trail is not only in the DNA of our own species (which often includes important genes inherited from Neanderthals) but also skeletons of hybrids.

Our sexy ancestors were mating with everything that looked vaguely human. Keep that in mind when the dudebros are whining about how Western women aren’t meeting their high standards of beauty. They’d fuck a chimp if one offered the opportunity.

However, many of the changes in our human evolutionary lineage maybe the result of chance.

For example, where isolated populations have a characteristic, such as some aspect of their appearance, which doesn’t make much difference to their survival and this form continues to change in descendants. Features of Neanderthals’ faces (such as their pronounced brows) or body (including large rib cages) might have resulted simply from genetic drift.

Oh, dear, the evolutionary psychologist won’t like that. Too bad, it’s true.

The origins of our own species coincided with major shifts in climate as we became more distinct from other species at these points in time. All other species of human seem to have died out as a result of climate change.

…and we’re next, at the rate we’re going.

The trail of human compassion extends back one and a half million years ago. Scientist have traced medical knowledge to at least the time of the Neanderthals.

Altruism has many important survival benefits. It enabled older community members to pass on important knowledge. And medical care kept skilled hunters alive.

We should have listened more closely to Kropotkin, rather than the imperialist colonizers who shaped the early perspectives on evolutionary theory. He was on to something (he also considered climate to be a critical evolutionary force.)

Evolution made us more emotionally exposed than we like to imagine. Like domestic dogs, with whom we share many genetic adaptations, such as greater tolerance for outsiders, and sensitivity to social cues, human hypersociability has come with a price: emotional vulnerabilities.

Counterpoint: Republicans and Tories. Human psychopaths seem to have a decided advantage in the acquisition of power.

Bret Weinstein used to teach evolutionary biology

It was a big win for Evergreen College to get rid of him, because he had to have been teaching it badly. This is the kind of obsolete adaptationist garbage he was teaching, and the kind of twisty reasoning he uses.

Let us begin the vivisection.

Foreskin is an evolutionary adaptation.

No, he does not know that. There is no evidence to suggest that it has any significant effect at all, in an evolutionary sense. There is no history of people born without foreskins in any kind of competitive interaction with people with them; there is no evidence of a differential reproductive advantage in any human lineages.

He’s making shit up. This is indicative of a crude adaptationist mindset where everything must have an adaptive effect.

It had a value and may or may not be net -beneficial in the modern environments

What value? Be specific. What change in value in modern environments has occurred?

Circumcision is also an adaptation that may/may-not be net-beneficial in modern times

Loss of a foreskin is not an adaptation — it’s not heritable. It’s a cultural trait. It’s effects are complex: sure, it may be important in establishing a group identity (a cultural phenomenon again!), but it probably has also led to some small number of babies bleeding out. So what if it may or may not be beneficial? It’s a thing. People also get ear piercings, or tattoos, or funny haircuts. Are those adaptations now?

All this adds up to Weinstein’s kicker.

Surgical sex change is not an adaptation. Done in children it’s immoral.

Alex up there hits the nail on the head. Why is one kind of modification (circumcision) adaptive, but another kind (gender affirmation) “immoral”? This is all just bad rationalization by Weinstein. I wonder if he has a sense of shame left any more?


Has nothing to do with preference. Circumcision has stood the test of evolutionary time. If it was simply negative, selection would have eliminated it.

There you have it: if it exists for some length of time, it is good and must have some advantage, or evolution would have eliminated it, because every bad thing is culled by the all-seeing perfect eye of natural selection. Migraines, bad knees, PCOS, religion, hernias, primogeniture, aging, the infield fly rule in baseball, wisdom teeth, vitamin C dependency, and war, all blessed by the flawless filter of evolution, or they wouldn’t exist anymore.

Good god, what a panadaptationist idiot. They really do exist. With bad logic and science like that, you know all he’s doing is signaling fallaciously to his bigoted anti-trans cronies.

But also, I have to wonder: why does he consider evolutionary consequences to be the only thing we consider when doing a thing? I blog because I enjoy it, not because it gives my offspring some advantage. You can like a rainbow or dancing or music or being in the company of friends because it makes you feel good — not everything is derived from some kind of biological calculus.

Not impressed by the Extended Evolutionary Synthesis

This article in the Guardian, “Do we need a new theory of evolution?” has it’s moments, but I hated the title and didn’t care at all for the opening. It’s true, scientists don’t know everything, but we know more than the author thinks.

Strange as it sounds, scientists still do not know the answers to some of the most basic questions about how life on Earth evolved. Take eyes, for instance. Where do they come from, exactly? The usual explanation of how we got these stupendously complex organs rests upon the theory of natural selection.

You may recall the gist from school biology lessons. If a creature with poor eyesight happens to produce offspring with slightly better eyesight, thanks to random mutations, then that tiny bit more vision gives them more chance of survival. The longer they survive, the more chance they have to reproduce and pass on the genes that equipped them with slightly better eyesight. Some of their offspring might, in turn, have better eyesight than their parents, making it likelier that they, too, will reproduce. And so on. Generation by generation, over unfathomably long periods of time, tiny advantages add up. Eventually, after a few hundred million years, you have creatures who can see as well as humans, or cats, or owls.

This is the basic story of evolution, as recounted in countless textbooks and pop-science bestsellers. The problem, according to a growing number of scientists, is that it is absurdly crude and misleading.

For one thing, it starts midway through the story, taking for granted the existence of light-sensitive cells, lenses and irises, without explaining where they came from in the first place. Nor does it adequately explain how such delicate and easily disrupted components meshed together to form a single organ. And it isn’t just eyes that the traditional theory struggles with. “The first eye, the first wing, the first placenta. How they emerge. Explaining these is the foundational motivation of evolutionary biology,” says Armin Moczek, a biologist at the University of Indiana. “And yet, we still do not have a good answer. This classic idea of gradual change, one happy accident at a time, has so far fallen flat.”

But we don’t take the existence of light sensitive cells for granted at all! It’s biochemistry. There are organic molecules that can absorb the energy of a photon and undergo a conformational change; there are single-celled organisms that can recognize the impact of light and change their behavior or biochemistry. We don’t need to explain any stepwise change in the properties of abiological materials, because that’s just physics or organic chemistry. Is evolutionary biology incomplete if it doesn’t argue that physics evolved? Are we allowed to understand that chemistry existed long before life?

The article spends a lot of time on the Extended Evolutionary Synthesis, giving it more credibility than it deserves, and plays up the drama of evolutionary theory changing, as if that wasn’t a normal scientific response to new evidence and ideas. Stuff like this doesn’t help.

Then came a devastating series of new findings that called into question the theory’s foundations. These discoveries, which began in the late 60s, came from molecular biologists. While the modern synthesists looked at life as if through a telescope, studying the development of huge populations over immense chunks of time, the molecular biologists looked through a microscope, focusing on individual molecules. And when they looked, they found that natural selection was not the all-powerful force that many had assumed it to be.

They found that the molecules in our cells – and thus the sequences of the genes behind them – were mutating at a very high rate. This was unexpected, but not necessarily a threat to mainstream evolutionary theory. According to the modern synthesis, even if mutations turned out to be common, natural selection would, over time, still be the primary cause of change, preserving the useful mutations and junking the useless ones. But that isn’t what was happening. The genes were changing – that is, evolving – but natural selection wasn’t playing a part. Some genetic changes were being preserved for no reason apart from pure chance. Natural selection seemed to be asleep at the wheel.

Evolutionary biologists were stunned.

“Devastating.” “Stunned.” Nah. There’s an ongoing argument about the relative importance of various processes, but no one was emotionally wrecked by the discovery that evolution is complicated. There are conservative scientists who refuse to budge or even acknowledge the existence of stuff like neutral theory, but they’re not particularly interesting. On the other side, there are wacky extremists with their hair on fire screaming that the existence of developmental plasticity means that we have to throw away everything. Most scientists see new phenomena and say, “Cool. Now how does this fit with that?”

The article links to a Nature article, “Does evolutionary theory need a rethink?”, and it takes an odd angle. It only mentions the EES side, but the Nature article had two sides, one answering the question with “YES, URGENTLY,” the other saying “NO, ALL IS WELL.” So the EES side sets everything up as deeply in opposition to the Standard Evolutionary Theory (SET) side.

In our view, this ‘gene-centric’ focus fails to capture the full gamut of processes that direct evolution. Missing pieces include how physical development influences the generation of variation (developmental bias); how the environment directly shapes organisms’ traits (plasticity); how organisms modify environments (niche construction); and how organisms transmit more than genes across generations (extra-genetic inheritance). For SET, these phenomena are just outcomes of evolution. For the EES, they are also causes.

Valuable insight into the causes of adaptation and the appearance of new traits comes from the field of evolutionary developmental biology (‘evo-devo’). Some of its experimental findings are proving tricky to assimilate into SET. Particularly thorny is the observation that much variation is not random because developmental processes generate certain forms more readily than others. For example, among one group of centipedes, each of the more than 1,000 species has an odd number of leg-bearing segments, because of the mechanisms of segment development.

Maybe I’m an oddball, but nothing there is in conflict. I learned about plasticity, niche construction, and epigenetics and just took them on as part of the process of evolution, working alongside familiar older ideas about changes in allele frequency. How can anyone think evo-devo is some radical competitor to evolutionary theory? It’s got “evolution” in the name! I’ve been following evo-devo for forty years now, and certainly in the early days some were over-enthusiastic, calling it revolutionary, but really, it’s simply part of evolution. I don’t need to chant slogans or demand wild changes in the textbooks, they’ve all been steadily bringing more and more content about these crazy ideas about mechanisms other than selection into the fold. Nusslein-Volhard and Wieschaus are in freshman college biology texts now!

But the EES fanatics are not satisfied.

The case for EES rests on a simple claim: in the past few decades, we have learned many remarkable things about the natural world – and these things should be given space in biology’s core theory. One of the most fascinating recent areas of research is known as plasticity, which has shown that some organisms have the potential to adapt more rapidly and more radically than was once thought. Descriptions of plasticity are startling, bringing to mind the kinds of wild transformations you might expect to find in comic books and science fiction movies.

Yes, plasticity exists, it’s really neat-o, I’ve read lots of papers on it, and I’m a big fan of Mary Jane West-Eberhard’s work. So? What does it mean, “given space in biology’s core theory”? I don’t understand. I open up an evolutionary biology textbook, and it takes hundreds of pages to explain how evolution works, and it includes plasticity, and punctuated equilibrium, and nearly neutral theory, and lots of ideas that explain a complex process. What is this “core theory”? They talk as if there is some tidy concise kernel that everything is derived from, and they want to wedge in some detail. That’s not how it works. That’s not how anything works. Maybe they should step back and explain accurately what this “core theory” is.

The Guardian article sort of redeems itself at the end by pointing out the obvious: what is this single “core theory” they want to modify? There isn’t one!

The computational biologist Eugene Koonin thinks people should get used to theories not fitting together. Unification is a mirage. “In my view there is no – can be no – single theory of evolution,” he told me. “There cannot be a single theory of everything. Even physicists do not have a theory of everything.”

This is true. Physicists agree that the theory of quantum mechanics applies to very tiny particles, and Einstein’s theory of general relativity applies to larger ones. Yet the two theories appear incompatible. Late in life, Einstein hoped to find a way to unify them. He died unsuccessful. In the next few decades, other physicists took up the same task, but progress stalled, and many came to believe it might be impossible. If you ask a physicist today about whether we need a unifying theory, they would probably look at you with puzzlement. What’s the point, they might ask. The field works, the work continues.

I’m not thrilled with bringing physics into the story. Most people don’t understand evolutionary theory, so trying to compare it to another complex field that most people don’t understand (including myself) is not helpful at all. I agree with Koonin on the evolution part, though: there are a lot of messy moving parts to evolution, why even try to claim that it’s all unified in one simple, clear principle? Embrace diversity and complexity. You’ll never get anywhere trying to claim ownership of the “core theory”.

That might be the real issue here. In 1859, one man, Darwin, could say “This is my theory,” (with a little nod to Wallace). In the mid-20th century, a massive mob of scientists could come up with something called the Neo-Darwinian Synthesis, but no one person could lay claim to it. It was too big and sprawling and crossed multiple sub-disciplines. Now a handful of people want credit for some half-assed idea they call the EES…sorry, people, it’s just some more tasty ingredients for the stew, it’s not replacing anything.

Somebody is going to have to revise the FAQ

In the Index to Creationist Claims, rebutting the claim by Henry Morris that No new species have been observed, it is written:

New species have arisen in historical times. For example:

A new species of mosquito, isolated in London’s Underground, has speciated from Culex pipiens (Byrne and Nichols 1999; Nuttall 1998).

This claim that a new species arose since the London Underground was built has been widely reported.

In 1999, an English researcher named Katharyne Byrne went underground to investigate further. When she compared Underground mosquitoes and compared them to others found in London houses, she learned that they were a distinct subspecies.

After ruling out migration from elsewhere in the continent, Byrne concluded that the London Underground was colonized by mosquitoes a single time, then achieved “reproductive isolation,” or barriers to reproduction with different species, in the subway tunnels.

“In the continent” is the critical phrase here. As it turns out, they didn’t look far enough afield — they needed to look at species in North Africa. The London Underground mosquito has a deeper history than the London Underground!

The northern house mosquito Culex pipiens sensu stricto is one of the most important disease vector mosquitoes in temperate zones across the northern hemisphere, responsible for the emergence of West Nile Virus over the last two decades. It comprises two ecologically distinct forms — an aboveground form, pipiens, diapauses in winter and primarily bites birds, while a belowground form, molestus, thrives year-round in subways, basements and other human-made, belowground habitats, bites mammals, and can even lay eggs without a blood meal. The two forms hybridize in some but not all places, leading to a complex ecological mosaic that complicates predictions of vectorial capacity. Moreover, the origin of the belowground molestus is contentious, with iconic populations from the London Underground subway system being held up by evolutionary biologists as a preeminent example of rapid, in situ, urban adaptation and speciation. We review the recent and historical literature on the origin and ecology of this important mosquito and its enigmatic forms. A synthesis of genetic and ecological studies spanning 100+ years clarifies a striking latitudinal gradient — behaviorally divergent and reproductively isolated forms in northern Europe gradually break down into what appear to be well-mixed, intermediate populations in North Africa. Moreover, a continuous narrative thread dating back to the original description of form molestus in Egypt in 1775 refutes the popular idea that belowground mosquitoes in London evolved in situ from their aboveground counterparts. These enigmatic mosquitoes are more likely derived from populations in the Middle East, where human-biting and other adaptations to human environments may have evolved on the timescale of millennia rather than centuries. We outline several areas for future work and discuss the implications of these patterns for public health and for our understanding of urban adaptation in the Anthropocene.

It’s still evolution, just evolution over millennia rather than less than a century.