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.

Larry Moran discovers the quicksand that is Wikipedia

I tell my students that they are not allowed to cite Wikipedia in their papers. Sure, you can browse it to get a general idea on a topic, but then you have to do the work of delving into the scientific literature to figure out what’s actually happening. There also doesn’t seem to be much validation of what Wikipedia does cite. The article on non-coding DNA still cites Nessa Carey! I read her book, and my god, it is a muddled mess of badly written pop pseudoscience.

Larry Moran is confident that Wikipedia is a useful resource and that it could be made better, so he waded into the morass and decided to try editing that non-coding DNA article. He’s a more optimistic person than I am. He decided to fix a lot of bad references made by people who don’t have a tenth the expertise on the subject he does…and discovers how they deal with interlopers.

The introduction has been restored to the version that talks about the ENCODE project and references Nessa Carey’s book. I tried to move that paragraph to the section on the ENCODE project and I deleted the reference to Carey’s book on the grounds that it is not scientifically accurate [see Nessa Carey doesn’t understand junk DNA]. The Wikipedia police have restored the original version three times without explaining why they think we should mention the ENCODE results in the introduction to an article on non-coding DNA and without explaining why Nessa Carey’s book needs to be referenced.

Nowadays, the only people I see citing ENCODE are creationists, so I am unimpressed that Wikipedia does not like people who can put the study in context. It seems to be official policy that no experts are allowed to edit bad wikipedia articles — they have a point of view, which is very bad.

Here is an editor, Ramos1990, explaining the rules to him.

There is no way to verify who you are on wikipedia. Many people claim to be famous people here so that is not an argument that is valid or carries any weight on wikipedia. And merely claiming it is not a reason for anyone to believe what you are saying either. On top of that if you really are Larry Moran then there is conflict of interest issues where you cannot push your POV on an article. Especially since there are other viewpoints on the matter, for instance Carey and Pennisi whom you want to get rid of an censor out of the article.

Hmmm. Larry was not claiming that you should believe him because he’s famous; Kim Kardashian is far more famous, but I don’t think she knows much about biochemistry. He’s saying he’s a reputable authority on a narrow topic. What wikipedia is saying is that they won’t do anything to verify a source, and if they did, they’d have to reject him because he has a POV. Which means that wiki editors are all fundamentally anonymous, and they have to pretend they don’t have a POV even when they patently do. It’s a weird situation.

Here, for instance, is the bio for Ramos1990.

The Sciences (esp. Chemistry), Engineering, Mathematics, History of Science, Sociology, Anthropology, Archaeology, Philosophy, Secularism/Religion, Atheism and other related stuff. The world has lots of good stuff to study.

That is not a catalog of their expertise. That’s a list of ‘stuff’ that interests them. They could be a bumbling dilettante or a brilliant polymath, and there’s no way to tell. But, apparently, all that matters is that they have no POV and can put up the illusion of impartiality, even on subjects where expertise is needed to sort out the complexities and make a reasonable assessment. The epistemology of Wikipedia is a very strange thing in which it is official policy that you are not allowed to know how anyone knows what they claim to know.

This comment on Larry’s site is worth noting:

The “corrections” at Wikipedia and the statement by the head of the NIHGR are certainly depressing. The both reflect the consensus among genomicists and molecular biologists. That in turn is based on their very limited grasp of molecular evolution. On the other side is the near-unanimous consensus among molecular evolutionists that there is lots of junk DNA. That is based on their actually understanding the processes of inserting junk and removing it. Unfortunately there are many more genomicists and molecular biologists, so the vote is still heavily against junk DNA. Wikipedia has the strength and the limitation that it is a dominant-consensus view, and we can see that in a case like this it serves to reinforce a wrong dominant consensus. Perhaps someday soon there will be a page on “Junk DNA controversy” in which the pro-junk side will get to edit the description of what we say. When the 2012 ENCODE disaster occurred, I predicted gloomily that it would take the field 10 years to get back to where it was. Those 10 years are nearly done, and things still look bad. I have more recently started telling people that it will take more like 20 years. Actually, 30 might be more like it.

Unfortunately, that was said by Joe Felsenstein, a world-renowned authority on molecular evolution, so it’s invalid in Wikipedia’s eyes.

I’ll be continuing to tell my students that Wikipedia is untrustworthy, and that they shouldn’t cite it, ever.

I needed a laugh

Awww. Mythicist Milwaukee got their Twitter account suspended, so they’re trying to take legal action to get reinstated. They’ve start a fundraiser that allows…well, I’ll let Thomas Smith explain it.

I like the Pray Now button. If I were to visit that site (I won’t), I’d click the Pray Now button for them.

By the way, as someone who has had to deal with lawyers before, a $2500 goal is paltry.

While they’re demolishing everything else, the Supreme Court might as well destroy separation of church & state

We got another grand decision today. The Supreme Court decided in favor of a public school football coach who pushed Christianity in his games. After all, it was just “quiet prayer” and a “brief thanks” at his games.

Nothing wrong with that! I have no objection to anyone expressing their faith privately, or in church. The problem is leading a group in prayer, but if Coach Kennedy wasn’t doing that, no problem.

Photograph of Coach Kennedy’s “quiet”, “brief” prayer:

OK, that’s one and done. Now we await the courts decision to gut the Environmental Protection Agency. Anyone want to guess how that one will go?

Jebus, but I detest his smug smirking face

But he’s right.

That’s exactly what the Supreme Court is trying to do, impose a Catholic Taliban on us…although the “Taliban” part is totally redundant. This is exactly what a purely, strictly, orthodox, traditional Catholicism wants, we don’t need to blame the Muslims for it.

You know, the Founding Fathers would have been horrified at the thought of women and Catholics on the court. It’s odd how these fanatical Originalists can ignore that.

Oh no, I was biologist-splained!

Getting into an argument on Reddit might be worse than arguing on Twitter. Some day I’ll learn.

Anyway, here was someone trying to claim that sperm aren’t alive, and that human life begins at conception.

When I agreed with the second quote and also pointed out that that 95% number is a made-up statistic, I got this insightful comment.

Well human life certainly does begin at conception…

You’re not a biologist, btw.

No one argues that a human zygote is something other than a human zygote. Unfortunately, I engaged with the clown claiming I’m not a biologist, and pointed out that those are also human sperm and human oocytes.

They were having none of that.

The question I always ask people who raise the claim that human life begins at conception…are human zygotes not the product of the fusion of human gametes? I

Yes… That’s what we call fertilization. Before conception the egg isn’t fertilized and only contains half of a human’s dna and only 23 chromosomes…

Human reproductive cells aren’t whole human organisms/human beings like a zygote is.

In biology, the zygote is called the cell of life because it usually is the first cell of a new organism. (since it’s basically a fertilized ovum.)

gametes are just the haploid stage of the human life cycle.

Yes… they are reproductive cells. Ofc, they’re haploid… Lol.

Are you sure you’re a biologist ’cause you sure don’t sound like one. Lmao.

I think I just got biologist-splained.

I also think they tripped over themselves. The whole argument rests on how we define what whole human organisms/human beings are. I agree that a sperm cell isn’t a human being. Neither is a zygote, or a blastula, or a gastrula, and neither is a fetus with an undeveloped nervous system and non-functional lungs and an inability to survive without its placenta. “Human” is a modifier used to designate the ancestry of a cell, and is not synonymous with “human being.”

But what do I know? I’m not a biologist!

Pacing about in the waiting room

I was sure today would be the day. As soon as I got out of PT, I rushed over to the lab, confident that finally my Steatoda triangulosa spiderlings would be emerging. Yesterday, I saw that they were getting dark hairs on their legs, although their bodies remain pale, and were making occasional feeble twitches, so I figured they’d be getting on with it shortly.

No such luck. The legs are getting darker, and the movements are much more robust. They’re packed tightly into the egg sac, so when you see one wiggle, there’s a wave of activity all across the sac. Any time now, he says again, as he has for the last several days.

Part of the reason for my eagerness is that I’m used to Parasteatoda — the spiderlings of that species emerge after less than 10 days, while these S. trangulosa eggs/embryos have been sitting there developing for 26 days so far. And P. tepidariorum will hatch out as many as a 100 babies at onces, while this species’ egg sacs will produce maybe 20 spiderlings. No wonder P. tep is the popular model system!

It makes me wonder how they can compete. P. tep is ubiquitous in houses; S. tri I find in houses, but also in ‘wilder’ environments. Maybe they’re simply being outcompeted for the most stable environment, or maybe S. tri spiderlings are better adapted, somehow, for more marginal spaces. I don’t know. I’m going to have to hatch out some P. tep and have them wrestle.

I’m also going to have to get some S. borealis egg sacs for comparison, but they’re turning out to be harder to breed in the lab.

I’m recording some day-by-day videos, and when the whole batch finally pops out, I’ll compile them all together and post them on YouTube…but I’ll be releasing them to my Patreon first.

I don’t have a ‘technical difficulties’ sign

The combination of an early morning physical therapy session and the need to go in to the lab as soon as that is done (today might be the day a big egg sac opens up and a spider swarm emerges — cross your fingers) means I’m going to be out of the blogging game for a while — I should be back later this morning. Until then, enjoy the Spider, illustrated with a picture of a cephalopod.

Damned if you do, damned if you don’t

I heard that the Bible has a recommendation for an abortion remedy, and I thought that was pretty cool, until I actually read it. Jesus, the Bible makes everything worse. Numbers 5:11-31.

11 And the Lord spake unto Moses, saying,

12 Speak unto the children of Israel, and say unto them, If any man’s wife go aside, and commit a trespass against him,

13 And a man lie with her carnally, and it be hid from the eyes of her husband, and be kept close, and she be defiled, and there be no witness against her, neither she be taken with the manner;

14 And the spirit of jealousy come upon him, and he be jealous of his wife, and she be defiled: or if the spirit of jealousy come upon him, and he be jealous of his wife, and she be not defiled:

15 Then shall the man bring his wife unto the priest, and he shall bring her offering for her, the tenth part of an ephah of barley meal; he shall pour no oil upon it, nor put frankincense thereon; for it is an offering of jealousy, an offering of memorial, bringing iniquity to remembrance.

16 And the priest shall bring her near, and set her before the Lord:

17 And the priest shall take holy water in an earthen vessel; and of the dust that is in the floor of the tabernacle the priest shall take, and put it into the water:

18 And the priest shall set the woman before the Lord, and uncover the woman’s head, and put the offering of memorial in her hands, which is the jealousy offering: and the priest shall have in his hand the bitter water that causeth the curse:

19 And the priest shall charge her by an oath, and say unto the woman, If no man have lain with thee, and if thou hast not gone aside to uncleanness with another instead of thy husband, be thou free from this bitter water that causeth the curse:

20 But if thou hast gone aside to another instead of thy husband, and if thou be defiled, and some man have lain with thee beside thine husband:

21 Then the priest shall charge the woman with an oath of cursing, and the priest shall say unto the woman, The Lord make thee a curse and an oath among thy people, when the Lord doth make thy thigh to rot, and thy belly to swell;

22 And this water that causeth the curse shall go into thy bowels, to make thy belly to swell, and thy thigh to rot: And the woman shall say, Amen, amen.

23 And the priest shall write these curses in a book, and he shall blot them out with the bitter water:

24 And he shall cause the woman to drink the bitter water that causeth the curse: and the water that causeth the curse shall enter into her, and become bitter.

25 Then the priest shall take the jealousy offering out of the woman’s hand, and shall wave the offering before the Lord, and offer it upon the altar:

26 And the priest shall take an handful of the offering, even the memorial thereof, and burn it upon the altar, and afterward shall cause the woman to drink the water.

27 And when he hath made her to drink the water, then it shall come to pass, that, if she be defiled, and have done trespass against her husband, that the water that causeth the curse shall enter into her, and become bitter, and her belly shall swell, and her thigh shall rot: and the woman shall be a curse among her people.

28 And if the woman be not defiled, but be clean; then she shall be free, and shall conceive seed.

29 This is the law of jealousies, when a wife goeth aside to another instead of her husband, and is defiled;

30 Or when the spirit of jealousy cometh upon him, and he be jealous over his wife, and shall set the woman before the Lord, and the priest shall execute upon her all this law.

31 Then shall the man be guiltless from iniquity, and this woman shall bear her iniquity.

Yikes. Sure, abortion is OK in the Bible, but just for a woman who is suspected of adultery by her husband, and if she’s found guilty of adultery, then her belly shall swell, and her thigh shall rot: and the woman shall be a curse among her people. I think maybe we shouldn’t be looking to the Christian holy book for guidance on this issue, or any other for that matter.

Maybe Xian hypocrisy is preferred to Xians being true to the Bible.

The Minnesota condition

Here’s what it’s like to live here when reproductive rights are being stripped everywhere around us: the governor sent out a bulk email.

Without Roe v. Wade as a safeguard, Minnesota could soon become the only state in the upper Midwest with safe and legal access to abortion.

We are a safe haven for reproductive freedom, and as long as I’m governor, it will stay that way. That’s why today, I signed an Executive Order to further protect people who get or provide legal abortions in Minnesota from possible legal repercussions in other states.

Lt. Governor Flanagan and I have been clear: We will not allow Donald Trump’s 6-3 conservative Supreme Court majority to set back our rights here in Minnesota.

Our Republican anti-choice extremist opponents, on the other hand, have pledged to ban abortion outright, with no exceptions even for rape or incest, the first chance they get.

That’s pretty good, and it’s true that the Republicans in this state are yowling about needing to prove they’re good ‘Muricans by imposing even more cruel and burdensome restrictions. It was marred, however, by the usual ‘give me money’ close. Sorry, you can ask for my vote, but not for donations. There are people who need them more. Like the Red River Women’s Clinic.

The only abortion clinic in North Dakota is now preparing to move across state lines following the recent Supreme Court ruling on Roe v. Wade.

Red River Women’s Clinic, located in Fargo, has been the only provider in the state for 20 years.
They now await closure, which will leave many women in the state without care.
Clinic Director Tammi Kromenaker told CNN Saturday they are still open, for now. “The plan is to provide service as long as we legally can,” Kromenaker said.

Fargo, if you don’t know your midwestern geography, is on the far eastern side of the state, right on the border with Minnesota, and Moorhead is a short hop across the river, so this is a relatively easy move. It’s still inconvenient and expensive. I’d rather donate to the clinic than to Democrats.

Unfortunately, as easy as it is to move, these assholes can also easily drive for 15 minutes to torment women. Sickos.

The people in the blue vests are heroes, clinic escorts. The people with the obnoxious signs are scum. I notice that the scum are allowed to cluster right around the entrance for maximum viciousness. Maybe the Minnesota Democrats could get their act together to pass a law setting much larger restrictions on how close harassers can get to a women’s health clinic? Maybe then they could ask me for a few bucks.