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.

Put your affairs in order, biologists. Your time is nigh!

We only have a month or two left. I have been reminded of a prediction made in the July/August 2004 issue of Touchstone magazine. Brace yourselves.

Where is the ID movement going in the next ten years? What new issues will it be exploring, and what new challenges will it be offering Darwinism?

Dembski: In the next five years, molecular Darwinism—the idea that Darwinian processes can produce complex molecular structures at the subcellular level—will be dead. When that happens, evolutionary biology will experience a crisis of confidence because evolutionary biology hinges on the evolution of the right molecules. I therefore foresee a Taliban-style collapse of Darwinism in the next ten years. Intelligent design will of course profit greatly from this. For ID to win the day, however, will require talented new researchers able to move this research program forward, showing how intelligent design provides better insights into biological systems than the dying Darwinian paradigm.

Man, I’m glad I’ll be on sabbatical. It’ll give me a year to patch up the radical changes I’ll have to make in all of my courses after the ID revolution comes. The rest of you are going to be coming back to rubble in September.

Although, I should also mention that the very next paragraph in that article is the one credible paragraph Paul Nelson ever wrote.

Nelson: Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a real problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as “irreducible complexity” and “specified complexity”–but, as yet, no general theory of biological design.

Almost five years on, still no theory.

Altenberg 2008 is over

Massimo Pigliucci has posted the notes, parts 1, 2, and 3, from the Altenberg meeting that was unfortunately over-hyped by the creationist crowd (no blame for that attaches to the organizers of this meeting). It sounds like it was a phenomenally interesting meeting that was full of interesting ideas, but from these notes, it was also clearly a rather speculative meeting — not one that was trying to consolidate a body of solid observations into a coherent explanation, but one that was instead trying to define promising directions for an expansion of evolutionary theory. That’s also the message of the concluding statement of the meeting.

A group of 16 evolutionary biologists and philosophers of science convened at the Konrad Lorenz Institute for Evolution and Cognition Research in Altenberg (Austria) on July 11-13 to discuss the current status of evolutionary theory, and in particular a series of exciting empirical and conceptual advances that have marked the field in recent times.

The new information includes findings from the continuing molecular biology revolution, as well as a large body of empirical knowledge on genetic variation in natural populations, phenotypic plasticity, phylogenetics, species-level stasis and punctuational evolution, and developmental biology, among others.

The new concepts include (but are not limited to): evolvability, developmental plasticity, phenotypic and genetic accommodation, punctuated evolution, phenotypic innovation, facilitated variation, epigenetic inheritance, and multi-level selection.

By incorporating these new results and insights into our understanding of evolution, we believe that the explanatory power of evolutionary theory is greatly expanded within biology and beyond. As is the nature of science, some of the new ideas will stand the test of time, while others will be significantly modified. Nonetheless, there is much justified excitement in evolutionary biology these days. This is a propitious time to engage the scientific community in a vast interdisciplinary effort to further our understanding of how life evolves.

That’s a little soft — there are no grand reformulations of the neo-Darwinian synthesis in there, nor is anyone proposing to overturn our understanding of evolution — but that’s what I expected. It’s saying that there are a lot of exciting ideas and new observations that increase our understanding of the power of evolution, and promise to lead research in interesting new directions.

Unfortunately, one reporter has produced an abominably muddled, utterly worthless and uninformed account of the Altenberg meeting that has been picked up by many crackpots to suggest that evolution is in trouble. This not only ignores a fundamental property of science — that it is always pushing off in new directions — but embarrassingly overinflates the importance of this one meeting. This was a gathering of established scientists with some new proposals. It was not a meeting of the central directorate of the Darwinist cabal to formulate new dogma.

Where one ignorant kook dares to assert her inanity, you know the Discovery Institute will stampede after her. Both Paul Nelson and now Casey Luskin have cited her lunatic distortions favorably. Luskin’s account is egregiously incompetent, as we’ve come to expect — he even thinks Stuart Pivar was an attendee. Pivar is an eccentric New York art collector, heir to a septic tank fortune, who has no training in science and whose “theory” is a nonsensical bit of guesswork that is contradicted by observations anyone can make in a basic developmental biology lab. He was not at the meeting. No one in their right mind would even consider inviting him to such a serious event. Maybe if it was a birthday party and they needed someone to make balloon animals, he’d be a good man to have on hand.

Now we can move beyond the garbled hype of the creationists. Pigliucci lists several concepts up there that have promise for further research, and that may help us understand evolution better. That’s the productive result of the meeting, and the only part that counts. Those concepts are also going to be discussed by many other scientists at many other meetings — even I talked about some of them recently — but don’t let the liars on the creationist side confuse you into thinking that the fact that scientists are talking about new ideas is a sign that evolution is in crisis. Talking about new ideas is normal science.

Ontogenetic depth

i-ccbc028bf567ec6e49f3b515a2c4c149-old_pharyngula.gif

One of the serious shortcomings of Intelligent Design is that it does nothing to provide any new or productive insights into the workings of biology. ID proponents seem to be at least vaguely aware of this failure, in that they do frequently claim to be thinking about working on a preliminary, tentative approach towards the beginnings of a potential research program (my paraphrase), but most of the effort has been directed towards political and legal enforcement of their ideas, rather than actually testing those ideas. One advantage of pursuing only legalisms is that they don’t give scientists anything to grapple. Invariably, when ID proponents do dip their toes in the scientific waters, they end up getting eaten by the sharks that lurk there.

One example: Paul Nelson, of the Discovery Institute, has been peddling a peculiar idea he calls “ontogenetic depth” as a scientific concept that emerges from Intelligent Design. To his credit, he has been presenting this idea in legitimate science venues, at the Geological Society of America and Society for Developmental Biology meetings. Note that getting on the program at these meetings is not subject to peer-review, so it is not automatically a recognition of merit that this work has been presented publicly. It is a good sign that Nelson is willing to expose his work to criticism, though.

I’m going to give it some criticism here. “Ontogenetic depth” is a developmental idea, and I’m a developmental biologist. Today I also get to play shark.

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A sloppy simulacrum of science

Go read this first rate summary of an ID meeting by one of its unsympathetic attendees. It’s genuinely bizarre. The talks by the ID proponents are frankly, complete garbage (not that the account is that blunt), which explains the message everyone got afterwards.

A few days after the meeting ended, we all received an email stating that the ID people considered the conference a private meeting, and did not want any of us to discuss it, blog it, or publish anything about it. They said they had no intention of posting anything from the conference on the Discovery Institute’s web site (the entire proceedings were recorded). They claimed they would have some announcement at the time of the publication of the edited volume of presentations, in about a year, and wanted all of us to wait until then to say anything. These actions made me aware of the extent to which the ID movement was willing to bear false witness in order to achieve its goals, and that kept me from falling prey to my empathy for the underdog.

A stealth science meeting? I’ve heard of requests to embargo discussion outside of a meeting until publication — which is reasonable, since many journals are jealous entities who demand that their submissions be virginal and unpublished anywhere else — but that’s not the case here. After reading the account, it’s clear that they’ve got no science and bad science, and really just want to control the release of information, so they can massage their PR and generate false impressions of scholarly work.

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