The problem of homology

We don’t get to see our granddaughter this morning — she’s getting her pediatric checkup today — so while sitting on my thumbs in my hotel room this morning, I threw together a video on the problem of homology, as misrepresented by Jonathan Wells and Paul Nelson. Seriously, they get it all wrong with tendentious misrepresentations.

There is a real problem of homology, because homology is rendered difficult to see by standard, naturalistic evolutionary processess. Wells and Nelson get it all exactly backwards. That homologies are obscured by the nature of evolutionary change is what we’d expect from evolutionary theory. It’s like how bioinformaticians will talk about the problem of long branch attraction; it’s a real problem, but it doesn’t imply that evolution is wrong, because it’s an expected effect of evolutionary change.

Likewise, evo-devo people will write long papers about the problem of homology, because the action of evolution obscures homologies and we have to struggle to see beyond it. Only a pair of buffoons would argue that it means evolution is false.

I don’t have a script for this one, because it’s just me talking extemporaneously in a dull hotel room, sorry. But I do have a good quote from Mary Jane West-Eberhard, and that’ll have to do if you don’t have the patience to listen to some geezer talking at a camera.

Changing characters do not march ever outward along the branches of a phylogenetic tree. While homology, parallelism, and convergence remain useful conceptual guides, they need to be seen against a background of continual reshuffling with a particulate, mosaic phenotype that renders linear terms like parallelism and convergence only approximate, and potentially misleading, descriptions of evolution.

Does a concept of mixed or partial homology just make a mess of homology? In fact, evolution makes a mess of homology.

Mary Jane West-Eberhard

Diagnostic features of the taxon

I’ve been reminding everyone for 12 years now that Paul Nelson made a specific, quantifiable creationist claim and failed to deliver a promised explanation. This is not unusual. Jeffrey Shallit describes the common elements of the so-called ‘scientific’ creationist, and it’s astonishing how widespread these traits are. One of them is their eagerness to make explicit claims coupled with a reluctance to actually back them up.

The illustrious Robert J. Marks II, professor at Baylor University, is an example of this last characteristic. Back in 2014, he made the following claim: “we all agree that a picture of Mount Rushmore with the busts of four US Presidents contains more information than a picture of Mount Fuji”. I wanted to see the details of the calculation justifying this claim, so I asked Professor Marks to supply it. He did not reply.

Nor did he reply when I asked three months later.

Nor did he reply when I asked six months later.

Nor did he reply when I asked a year later.

It’s now been two years. Academics are busy people, but this is pretty silly. Who thinks the illustrious Professor Marks will ever show me a calculation justifying his claim?

That sounds so familiar. Maybe if you wait 13 years he’ll show you a calculation? Hope springs eternal!

You can see God sees even the sparrow fall oozing between the lines

sieve

This must be how creationists think a sieve works. The smaller particles see from a distance that they’ll fit through the holes, so they make a beeline for them, while the bigger particles that won’t fit recognize that fact and get out of their way. Adding more material to be filtered reduces the effectiveness of the sieve because the bulk hampers their ability to find their way to the face of the sieve.

You may laugh, but I have to conclude that this is the inevitable rationale that they’d have to make, given their inability to think statistically and impose teleology on every explanation of natural phenomena. So Wolf-Ekkehard Lönnig raises a most peculiar argument against evolution. Populations are too large.

…in the 1950s, French biologists, such as Cuénot, Tétry, and Chauvin, who did not follow the modern synthesis, raised the following objection to this kind of reasoning (summed up according to Litynski, 1961, p. 63):

Out of 120,000 fertilized eggs of the green frog only two individuals survive. Are we to conclude that these two frogs out of 120,000 were selected by nature because they were the fittest ones; or rather — as Cuenot said — that natural selection is nothing but blind mortality which selects nothing at all?

Similar questions may be raised for the 700 billion spores of Lycoperdon, the 114 million eggs multiplied with the number of spawning seasons of the American oyster, for the 28 million eggs of salmon and so on.

He doesn’t think evolution can work, because how can it possibly find the two best individuals out of a group of hundreds of thousands or millions? And the problem becomes worse the bigger the population!

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David Klinghoffer whines about an imaginary foul

fakeinjury

Uh-oh. I’ve disappointed David Klinghoffer. I should probably put that on my CV.

You see, the other day he praised a fellow named Tom Gilson for a post in which he provided a succinct summary of Intelligent Design creationism, and I took that summary apart, point by point. You might think, perhaps Klinghoffer finds fault with my analysis? He doesn’t provide any rebuttals. Did I get something wrong in using Gilson’s definition of ID? Nope, he doesn’t say…that would be hard to do anyway, since Klinghoffer praised it as exactly accurate!, exclamation point and all. Even in his title he declares that Tom Gilson Nails It.

So what’s his complaint? That I corrected the wrong person.

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The wisdom of worms

nematode

In my previous post about Paul Nelson’s weirdly ignorant view of nematode evolution, Kevin Anthoney made a prescient comment:

Remember that Nelson’s got this bizarre linear view of evolution which starts with a single cell creature, which evolves into a creature with a few cells, which evolves into one with a few more cells, and so on until you reach the 1031 cells in the nematode today. It wouldn’t surprise me at all if Nelson thought that the creature at the 150 cell stage in this process had to be like a modern nematode at the 150 cell stage of development.

The Discovery Institute has responded. I got as far as the massive projection in the following paragraph before giving up.

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Nematodes are not designed, they evolved

nematode

The latest fatuous obsession by Paul Nelson, Philosopher of Biology at the Discovery Institute, is a real corker. He has decided that nematodes could not possibly have evolved, because scientists (real ones, not creationist pseudoscientists) have produced an extremely detailed literature documenting their development; because Brenner, Horvitz, and Sulston (no creationists among them) won the Nobel Prize for their work describing the cell lineages to produce the worm; and because he doesn’t understand developmental biology at all. I’ve got palm impressions in my forehead from smacking myself so many times while watching this terrible little video.

This is why Paul Nelson is laughed at by developmental biologists. He cannot be taken seriously. I figured, though, that if you’re not already familiar with concepts and details of development, you might find him credible — he’s so pompously earnest! — so I thought I’d explain all the ways he goes wrong.

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In which creationists make me giddily, joyfully gleeful!

Oh boy oh boy oh boy oh boy. This is wonderful news, happy happy joy joy, gosha’mighty, I’m wiggling in my chair like a tickled puppy. What has made me so happy, you might ask?

A week from today I’m going to be speaking at the Crystal Palace in Glasgow, Scotland. I’ll be talking about the developmental evidence for evolution, and it should be great fun.

But that’s not the exciting news.

Glasgow has its very own Centre for Intelligent Design, and a fine collection of know-nothings it is. And they are being encouraged to attend my talk! So maybe there will be a contingent of critics present — and they can’t be as dumb as Rabbi Moshe Averick, can they? Yeah, they probably can be.

But that’s not the thrilling news, either.

The fun part is that the nitwits at Uncommon Descent have posted 10 + 1 Questions For Professor Myers, and are urging the Scottish creationists to show up and confront me with their stumpers.

And they’re SCREAMINGLY STUPID!

I read them with increasing disbelief: every single one of them was trivial and inane, and do nothing but reveal the ignorance and arrogance of the questioner. Every single one. Every one is built around some bizarre creationist misconception, too.

Please please please please please please, O Creationists, show up and ask me these questions. Pick any of them. Pick the one you are absolutely certain will make me squirt hot tears of frustration and despair right there on the stage. I’m begging you. Give me the opportunity to give you a public spanking. Oh, happy monkey, I will be delirious with joy if you try to make me suffer with these questions. They’re like a gift, a gift of idiocy.

Now I’m not going to answer them here just yet — I want to give the creationists a chance to slam me with ’em first. But I’ll post the answers next week, after they’ve taken their shot. If they do. I’m afraid they’ll be too cowardly to announce themselves in public like that.

Just so you can see them without going to that cloaca of creationism, Uncommon Descent, I’ve also posted the full set of questions below the fold. Go ahead and try to answer them if you’d like, but really, all of the answers to everyone of them was already tripping off my brain as I read them.

Hey, and show up in Glasgow. I can tell already it’s going to be a blast.

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Intelligent Design creationism is fundamentally wrong

Via Sandwalk, this is a clip of Paul Nelson praising Jonathan Wells and his godawful gemisch of bad scholarship and lies, Icons of Evolution. They were making a big to-do over the ten-year anniversary of publication of this ghastly hackwork, and here Nelson is piously praising the premise.

It’s infuriatingly dishonest. Notice what he repeats over and over: the textbooks “diverge from the actual evidence,” they’re “out of touch with the actual evidence,” we “need to take these standard stories back to the evidence.” This, from the Discovery Institute, a propaganda mill with no evidence for their fantasies about design at all. There is such an egregious disconnect between what Nelson says and what he and his cronies do that I half-expected his sanctimonious head to explode. If you’re an intelligent design creationists, you do not have the privilege of hectoring others about evidence.

Furthermore, he’s spewing this nonsense in praise of Icons of Evolution, a book to which honesty and evidence are words in a strange foreign language…yet Nelson claims the message of that book is that textbook authors need to be “scrupulous about accuracy” — and yet those scruples are never applied to Wells, and further, Nelson is more than a little self-serving here: he is co-author on another awful DI production, Explore Evolution, which is little more than a warmed-over edition of Icons, and which has also been panned in reviews.

And then Nelson says the “response was much more hostile than I would have guessed.” He claims the hostility was because they were airing “dirty laundry,” which is simply wrong. The hostility derived from the fact that it was an appallingly bad work of misrepresentation and misleading innuendo, all on the service of an intellectually bankrupt theology.

On top of Icons of Evolution and Explore Evolution, Wells rehashed the same lies again in The Politically Incorrect Guide to Darwinism and Intelligent Design. It’s become obvious that the Wells has gone dry: he’s simply repeating the same errors and phony arguments over and over again. This is not a man or work that warrants praise, but only condemnation and contempt.

In the past, I’ve focused on one specific issue that Wells repeatedly brings up, the idea that Haeckel’s embryos are some kind of ongoing problem for evolution. There are a lot of articles on Pharyngula on this subject, but I’ll just point to this one omnibus summary of links to articles on Haeckel and Wells, and briefly explain the nature of this ‘controversy’. There is a 19th century observation, made by multiple scientists and easily replicated today, that embryos go through a period called the phylotypic stage (and in vertebrates, called the pharyngula stage), in which species within a phylum exhibit a remarkable degree of similarity to one another. This is simply a fact: stop by my lab and I can pull out a series of slides of birds and mammals and reptiles and fish and show you how they all exhibit a set of characters, the presence of a tailbud and pharyngeal arches and somites and so forth, that are the hallmark of this relatively well-conserved stage. Now in the 19th century, Haeckel over-interpreted them to postulate a recapitulation of evolution within the development of an embryo, an idea now known to be false; Wells strategy has always been to point to an obsolete and falsified explanation for the similarities to argue that the evolutionary relationships are untenable. It’s a sleazy sleight of hand. Recapitulation theory is not in any way endorsed any more, but the similarities at the phylotopic stage are undeniable…yet Wells condemns any textbook that even shows photos of embryonic similarities.

That’s the central problem here. We have a phenomenon, the similarities between embryos at one stage of development, for which the creationists have no explanation, so they’re reduced to frantically denying the phenomenon. This isn’t the way science should work. The phenomenon is real; that these common similarities between embryos is better explained by common descent than by design may make creationists uncomfortable, but what a scientist should do is find an answer, not try to wave the problem away (or worse, accuse everyone who has seen these similarities as guilty of fraud).

I’d go further than to argue that the creationists are trying to hide data that defies their ideology. They’re trying to bury something that is almost paradigmatic of juicy, exciting science. There are a couple of properties of significant scientific questions that I consider emblematic of exactly the kind of work that is of great value.

  1. It has to address a universal phenomenon. The problem of phylotypy isn’t representative of all of life by any means, but it seems to be a near-universal within the animal kingdom. Why do organisms as diverse as insects and mammals exhibit this morphological bottleneck in their development? It’s a great question; it doesn’t deserve to be swept under the rug as the creationists would like to do.

  2. It has to be a non-trivial problem. Trying to figure out exactly what is going on in phylotypy isn’t easy, because the current best hypotheses all involve interactions within complex gene networks, not the most tractable problem, and solving it will require both comparative and computational tools. It’s the complexity of the subject that makes it both challenging and rewarding to solve.

  3. One thing guaranteed to spur interest if the postulated mechanisms are controversial. Proposed mechanisms for phylotypy are non-Darwinian: they involve selection for intrinsic properties of networks of developmental genes that establish large scale properties of embryonic patterning. Notice that it isn’t anti-Darwinian, or the creationists would be happy with it; the mechanism fits within the context of our understanding of evolution, but extends it somewhat to include conservation of a kind of sophisticated, modular array of genes that work together to build the body plan. It’s not just the alleles that matter, but the connections between them.

  4. Maybe I should have mentioned this one first. A key quality of good science is that it is doable — we have to be able to sit down and do measurements and experiments. Truth be told, a lot of ordinary science doesn’t engage the first three principles I listed above as much as it permits the rapid and routine collection of data. The phylotypy hasn’t been quite so tractable, and to move beyond a kind of morphological phenomenology that has characterized much of the work so far, requires comparative analysis of large dataset of developmental gene expression data. Until recently, that kind of information simply hasn’t been available.

I used the past tense there: that data hasn’t been available. But that’s changing fast now with new techniques in molecular and developmental biology, and later today I’ll summarize a couple of beautiful recent articles that have revealed some of the underpinnings of the phylotypic stage. The creationists weren’t just wrong, they’re on the wrong side of history, and day by day they are bing shown to be increasingly far off base.

Michael Ruse—Is Darwinism past its ‘sell by’ date? The challenge of evo-devo

How can I resist an opportunity to see Ruse gibbering on the stage? I’m curious to see whether he annoys or enlightens. It could go either way.

He’s not going to talk about evo-devo! OK, I’m already annoyed.

Criticizes the infamous New Scientist cover, “Darwin Was Wrong”; received email from Paul Nelson (boo) claiming the edifice of darwinism is crumbling; Rudy Raff has written that evolution requires development to remain relevant. Are today’s evolutionists genuinely Darwinian or not?

Plans to pick on something that was self-consciously in Darwin’s thinking. Darwin became an evolutionist in 1837 while analyzing the specimens he had collected on his voyage; he became a Darwinian in 1838 when he realized the mechanism of adaptive change, natural selection.

William Whewell was a major influence. Whewell tried to define good science: identifying a true cause, which is a hypothesis that explains the evidence. Darwin doesn’t see evolution at work, but the evidence is marshalled to point to the hypothesis. He’s not doing the original research, but picking it up and putting it together in a new and powerful way. Fossils, biogeography, homology, embryology, etc. all were assembled to support his theory.

Did Darwin trigger a paradigm shift? Huxley didn’t appreciate natural selection at all. It took the rediscovery of Mendel, popgen, etc. to bring about a major appreciation of the theory. Further revision with the synthetic theory that incorporated molecular biology.

Positively reviewed Dawkins’ latest book, and Dawkins is contemptuous of eyewitness testimony, but says the theory demands respect because of the volume of evidence, which is clearly in the spirit of Darwin and Whewell.

EO Wilson’s work on ants show the amazing specialization of castes in particular distributions. This is material Darwin never considered, but Wilson is using the tools of evolutionary biology to explain his hypotheses.

Pre-Cambrian was terra-incognito to Darwin; he had many ad hoc hypotheses to explain why we don’t have specimens from that era. Modern explanations do a better job of fitting the pre-Cambrian into a Darwinian framework.

We know much more about human evolution, extinction, geographical distributions (plate tectonics) than Darwin did, but these are still thoroughly explained by Darwin’s ideas.

Hox genes show deep homology between flies and humans, also interpreted in a Darwinian context.

Draws an analogy with the Volkswagen, which was completely different between the 40s and modern day, with no parts that are identical, and yet it is obviously linked. We will still be celebrating Darwin 100 years from now because we will still be using his ideas.

OK, not bad, not too annoying. Needed more evo-devo. Philosophers sure do talk a lot; this talk was definitely not as information-dense as the biology sessions.

Zimmer and Carroll say adios to Bloggingheads

I’ve always rather liked Bloggingheads — at least the idea of it, with one-on-one discussions between interesting people. It flops in execution often, since some of the participants wouldn’t recognize reason and evidence if it walked up and slapped them in the face with a large and pungent haddock (the right-winger political discussions are unwatchable, and it’s always had this problem of giving people like Jonah Goldberg a platform), but their Science Saturday has been generally good. I don’t always agree with the people they have on, but at least they’re interesting and provocative. And Sean Carroll and Carl Zimmer have been superstars of the format.

That’s changed lately. First they brought on Paul Nelson and Ron Numbers in a tawdry self-congratulation session that never addressed the Paraceratherium looming over the dialog, Nelson’s insane young earth creationism. Then most recently they brought in Michael Behe, squirrely academic front for the ID creationism movement, and again they let his inanity slide by bringing in a friendly conversationalist, the linguist John McWhorter, who fawned over Behe’s recent bad book.

What is this? Is bloggingheads to become a creationist-friendly site, where crackpots get to play talking head for a while and never risk getting their stupid ideas criticized? This is not good. If they want to bring in creationists, fine…but don’t give them a free pass on their foolishness by pairing them with people who can’t argue with the biology.

There was apparently some restlessness in the ranks of the regulars, and they had a conference call with Robert Wright, the man behind bloggingheads, which did not conclude at all satisfactorily. Now two of the best science people they had on call have declared that they will no longer be contributing.

Sean Carroll says goodbye for good reason.

What I objected to about the creationists was that they were not worthy opponents with whom I disagree; they’re just crackpots. Go to a biology conference, read a biology journal, spend time in a biology department; nobody is arguing about the possibility that an ill-specified supernatural “designer” is interfering at whim with the course of evolution. It’s not a serious idea. It may be out there in the public sphere as an idea that garners attention — but, as we all know, that holds true for all sorts of non-serious ideas. If I’m going to spend an hour of my life listening to two people have a discussion with each other, I want some confidence that they’re both serious people. Likewise, if I’m going to spend my own time and lend my own credibility to such an enterprise, I want to believe that serious discussions between respectable interlocutors are what the site is all about.

Carl Zimmer also departs.

My standard for taking part in any forum about science is pretty simple. All the participants must rely on peer-reviewed science that has direct bearing on the subject at hand, not specious arguments that may sound fancy but are scientifically empty. I believe standards like this one are crucial if we are to have productive discussions about the state of science and its effects on our lives.

This is not Blogginghead’s standard, at least as I understand it now. And so here we must part ways.

This is good, principled action, and it’s exactly what we need to do every time some journalistic enterprise tries to generate a false equivalence between serious science and crackpottery like creationism — shut them out. Say goodbye. Let the credible sources wash their hands of them and move on.

I’m still somewhat sympathetic to the idea of bloggingheads — and David Killoren left a good comment that basically admits that they screwed up — but there has to be a commitment to good science from the top down for it to work. I’m not convinced by the replies Wright has left on those two sites that he has that goal in mind.