Complex eyes in the Cambrian

I got a letter from a creationist today, claiming that “Darwinism is falsified,” based on an article in Nature. It’s kind of amazing; this article was just published today, and the metaphorical digital ink on it is barely metaphorically dry, and creationists are already busily mangling it.

It’s a good article describing some recent fossil discoveries, found in a 515 million year old deposit in South Australia. Matthew Cobb has already summarized the paper, so I’ll be brief on the details, but it’s very cool. What was found was a collection of arthropod eye impressions, probably from cast-off molts. No sign of the bodies of these animals was found, suggesting that perhaps they were not fully sclerotized, or as the authors suggest, that disarticulated eyes were more prone to rapid phosphatization than eyes attached to a decaying body. There is no evidence of biomineralization, so these were animals with a very light armor of chitin alone.

What’s wonderful about the eyes is that they are relatively large and contain numerous ommatidia, the individual facets of a compound eye. They have over 3,000 lenses, and there’s also evidence of regional specialization in the eye. These were highly visual animals that were capable of forming a good image of the world around them.

Complex arthropod eyes from the Early Cambrian. a-d, Three fossils of compound eyes from a large arthropod from the Emu Bay Shale, South Australia (a-c), shown in similar hypothesized orientation to the compound eye of a living predatory arthropod, the robberfly Laphria rufifemorata
(d; anterior view of head). All fossil eyes have large central ommatidial lenses forming a light-sensitive bright zone, b, and a sclerotized pedestal, p. Because the fossil eyes are largely symmetrical about the horizontal axis, it is not possible to determine dorsal and ventral surfaces, and thus whether the eyes are left or right. All fossils are oriented as if they are left eyes (medial is to the left of the figure). In b there is a radial tear (white line) with the top portion of the eye displaced downwards to overlie the main part; extensive wrinkling causes some central lenses (arrow) to be preserved almost perpendicular to the bedding plane.

These eyes are also from the early Cambrian, so they appeared in the early stages of large animal evolution. The closest thing to them in ommatidial number are the sophisticated eyes of many trilobites, but even there, these eyes were early and relatively large.

Complexity of the Early Cambrian Emu Bay Shale eyes compared to eyes in other early Palaeozoic taxa. a, b, Number of ommatidia (a) and lens size (b) plotted against stratigraphic age for Cambro-Ordovician arthropods. The Emu Bay Shale eyes have many more ommatidia and much larger individual ommatidia than eyes in all other Cambrian taxa. Trilobites are plotted according to eye type: schizochroal eyes have relatively few, large lenses and are optically unusual compared to typical compound eyes.

Where in this is the refutation of evolution? I don’t know. But I did receive a letter from that Canadian idiot, David Buckna, crowing about it, and linking to his very silly creationist article describing it, in which you’ll find the abstract for the paper with curious random spastic boldfacing added which supposedly highlight the parts of the story that contradict evolutionary theory, words like “complexity” and “Cambrian explosion” and “more complex” and “great evolutionary event”. It’s a bit bizarre and like looking at the obsessive activity of a squirrel gathering nuts.

Here’s the creationist summary of the paper, however.

The Cambrian explosion is affirmed; complexity appears suddenly without transitions; Darwinism is falsified; the inference to the best explanation is intelligent design. Let the world know.

Let’s deal with each of these claims one by one.

  1. The “Cambrian explosion” is a term coined by scientists to describe the rapid (in geological terms) appearance of large, complex animals with hard skeletons over the course of a few million years roughly half a billion years ago. There is no creationist gotcha in pointing out the existence of this geological period; scientists have written whole books on the subject.

  2. The sudden appearance of complexity is no surprise, either. We know that the fundamental mechanisms of eye function evolved long before the Cambrian, from the molecular evidence; what happened here was not that, poof, eyes instantly evolved, but that the evolution of body armor gradually increased from the pre-Cambrian through the Cambrian, making the organization of eyes visible in the fossil record.

    It is also the case that the measure of complexity here is determined by a simple meristic trait, the number of ommatidia. This is not radical. The hard part in the evolution of the compound eye was the development of the signal transduction mechanism, followed by the developmental rules that governed the formation of a regular, repeating structure of the eye. The number of ommatidia is a reflection of the degree of commitment of tissues in the head to eye formation, and is a quantitative difference, not a qualitative one.

    And finally, there’s nothing in the data from this paper that implies sudden origins; there can’t be. If it takes a few hundred thousand years for a complex eye to evolve from a simple light sensing organ, there is no way to determine that one sample of a set of fossils was the product of millions of years of evolution, or one day of magical creation. It’s a logical error and a failure of the imagination to assume that these descriptions are of a population that spontaneously emerged nearly-instantaneously.

  3. “Darwinism” is not falsified. Darwin himself explained in great detail how one should not expect fine-grained fossil series, due to the imperfection of the geological record. Creatonists, read chapter 9 of the Origin; here’s a brief excerpt.

    It should not be forgotten, that at the present day, with perfect specimens for examination, two forms can seldom be connected by intermediate varieties and thus proved to be the same species, until many specimens have been collected from many places; and in the case of fossil species this could rarely be effected by palaeontologists. We shall, perhaps, best perceive the improbability of our being enabled to connect species by numerous, fine, intermediate, fossil links, by asking ourselves whether, for instance, geologists at some future period will be able to prove, that our different breeds of cattle, sheep, horses, and dogs have descended from a single stock or from several aboriginal stocks; or, again, whether certain sea-shells inhabiting the shores of North America, which are ranked by some conchologists as distinct species from their European representatives, and by other conchologists as only varieties, are really varieties or are, as it is called, specifically distinct. This could be effected only by the future geologist discovering in a fossil state numerous intermediate gradations; and such success seems to me improbable in the highest degree.

    Finding a fossil eye with numerous ommatidia a hundred million years after molecular biology tells us that eyes evolved does not in any way falsify the idea of a gradual evolution of the eye.

  4. Given that there is nothing in this story that contradicts the idea of a natural process generating increasing complexity over time, and given that it’s an observation that fits perfectly comfortably within the body of evolutionary theory, there is no reason to leap the utterly unfounded conclusion that an invisible spirit zapped these fossils into existence — an invisible spirit for which there is no evidence. Furthermore, what evidence is in this paper directly contradicts Buckna’s beliefs: he is a young earth creationist, and this is a paper describing organisms that lived 515 million years ago. If you look at the chart I reproduced above, you might also notice that the pattern of complexity (ommatidial numbers) in trilobites shows a trend of increase over 80 million years.

  5. I shall gladly let the world know that David Buckna is an irrational fool who doesn’t know how to read a scientific paper and makes illogical leaps in his arguments.

Lee MSY,
Jago JB,
García-Bellido DC,
Edgecombe GD,
Gehling JG
Paterson JR (2011) Modern optics in exceptionally preserved eyes of Early Cambrian arthropods from Australia. Nature 474: 631-634.

It’s always good to go straight to the source

I tell other scientists all the time that their work is being appropriated by creationists who barely understand it, and that it is getting distorted to support bogus pseudoscience. Whenever you see a creationist quote a genuine science paper, you can pretty much trust that it is going to be mangled beyond recognition.

For instance, Jonathan MacLatchie raised a peculiar collection of questions to grill me with; here’s one of them.

9) If, as is often claimed by Darwinists, the pharyngeal pouches and ridges are indeed accurately thought of as vestigial gill slits (thus demonstrating our shared ancestry with fish), then why is it that the ‘gill-slit’ region in humans does not contain even partly developing slits or gills, and has no respiratory function? In fish, these structures are, quite literally, slits that form openings to allow water in and out of the internal gills that remove oxygen from the water. In human embryos, however, the pharyngeal pouches do not appear to be ‘old structures’ which have been reworked into ‘new structures’ (they do not develop into homologous structures such as lungs). Instead, the developmental fate of these locations includes a wide variety of structures which become part of the face, bones associated with the ear, facial expression muscles, the thymus, thyroid, and parathyroid glands (e.g. Manley and Capecchi, 1998).

You might be wondering about what that paper actually says, and you should. Never trust a creationist! And here’s where I get to pull Marshall McLuhan into the frame from offscreen.

Nancy Manley of the University of Georgia wrote to me today.

As a fan of both your website and of the pharyngula stages of development, I was intrigued to see the questions posed to you by ID followers before your recent talk. And kind of surprised, and bit taken aback, when one of my postdoctoral papers was cited in one of the questions – I am the Manley of Manley et al.

Since the ID questioners used a reference to one of my papers in the question, and this is actually an issue I am personally interested in from a scientific point of view, I feel compelled to answer also. In a way, it is ironic that they used this paper to illustrate their question, since it was our analysis of the pharyngeal pouch phenotype of the Hoxa3 null mice that led to our own interest in why terrestrial animals don’t have gills, and how the thymus and parathyroids may have evolved. We hypothesized that the evolution of morphology in the pharyngeal region (i.e. loss of gills and gain of pouch-derived organs like the thymus and parathyroids) was due to changes in the expression and/or function of the Hoxa3 gene. This hypothesis was proposed in a book chapter that I co-authored (Manley, NR and CC Blackburn. Thymus and Parathyroids. In Handbook of Stem Cells, Vol. 2: Embryonic Stem Cells, R. Lanza (Ed). Academic Press, 2004 v. 1:pp 391-406). I even obtained an NSF grant (now defunct) to test this hypothesis, and recently published a paper in the Proceedings of the National Academy of Sciences about it (Chen, et al., 2010, PNAS 107(23):10555-10560). We haven’t solved the problem yet, but the data so far indicate that changes in both the expression and function of Hoxa3 may have been involved in the evolution of pharyngeal region derivatives during vertebrate evolution, including loss of gills and development of pharyngeal pouch-derived organs.

I wish I could magically pull scientists out of a hat every time some po-faced creationist stooge raises a hand at one of my talks and starts lecturing me on their memorized quotes from the scientific literature. They always get them wrong.

By the way, I’ve been playing a game with MacLatchie. Every time I look into one of his citations, I go to google and type in both the author’s name and that of Harun Yahya, the Turkish creationist. It’s amazing — every time, I get a couple of quotes from one of his books, and they’re almost exactly the same as MacLatchie’s comments.

For example,
Harun Yahya also cites Manley. Compare this with what MacLatchie wrote, above.

Those human emryonic “gill slits” are just another Darwinian myth. These pharyngeal pouches do not develop into homologous structures such as lungs or gill-like structures. The developmental fate of these pouches include a wide variety of structures that become parts of the face, ear cavities, bones of the middle ear, muscles of masticulation and facial expression, the lower jaw, certain neck parts, and the thymus, thyroid, and parathyroid glands. (Manley, N.R. and Capecchi, M.R., Developmental Biology, 195 (1):1-15, 1998)

Isn’t this just weird? Now Yahya is a notorious plagiarist who rips off everything he’s written from the Christian creationist literature, and I don’t think MacLatchie is getting it from him. On the other hand, MacLatchie is a nobody, so I don’t think Yahya stole it from him. I think there’s another creationist source book somewhere, which both are borrowing from to make their claims, and I’m itching to know what it is.

The one thing I know for sure is that neither MacLatchie nor Yahya are at all original or creative, and that both are just trained parrots echoing some other source. If anyone recognizes where these claims are coming from, let me know — I’d like to go straight to the original compendium of nonsense and prune it at the root.

You go, Harry Lonsdale!

Harry Lonsdale is a godless Oregonian who has just offered a $50,000 prize plus $2,000,000 in funding for research into the origins of life.

A millionaire scientist who once ran as a Democratic nominee for the U.S. Senate has just launched a $50,000 prize to promote research on the origin of life. Yes, he has an ulterior motive: He hopes that researchers working on the question will eventually prove that life’s origins can be fully explained by physical and chemical processes, without invoking a creator.

Harry Lonsdale is a chemist in Bend, Oregon, who made a fortune when he sold his drug development and research company to Pfizer more than 25 years ago. Since then, he has leveraged his wealth for social, civic, and political causes, including a series of unsuccessful bids to become a U.S. senator. The 79-year-old Lonsdale is an avowed atheist who has advocated for gay rights, campaign finance reform, and environmental protections. Now, he’s on a mission to accelerate the quest to understand how life originated. Over the past 2 weeks, Lonsdale has taken out ads in Science, Nature, and Chemical and Engineering News announcing an Origin of Life Research Award that includes $50,000 for the best proposal to study the origin of life and up to $2 million in potential funding to carry out the work.

This is serious stuff, with serious people (like Jack Szostak) backing it, and another thing that is cool about it is that Lonsdale openly admits that his atheism is a motivation for funding science. The website for the project explains exactly what he’s looking for.

All submissions will be reviewed by a panel of scientific experts. Submissions should contain a statement of work to be performed and a letter of institutional support where appropriate. Submissions that suggest a multidisciplinary approach should describe how the necessary research capabilities will be provided. Submissions that rely on extraterrestrial sources of key materials must describe in detail how those materials would have been generated. Submissions involving the supernatural or that violate physical laws will not be considered.

That last clause is a given for all scientific research — it’s just rare to see it so clearly said.

Jonathan MacLatchie really is completely ineducable

It’s like talking to a brick wall: MacLatchie is appallingly obtuse. When last I argued with him, I pointed out that the major failing of his entire developmental argument against evolution was that it was built on a false premise. As I said then,

I can summarize it with one standard template: “Since Darwinian evolution predicts that development will conserve the evolutionary history of an organism, how do you account for feature X which doesn’t fit that model?” To which I can simply reply, “Evolution does not predict that development will conserve the evolutionary history of an organism, therefore your question is stupid.” It doesn’t matter how many X’s he drags out, given that the premise is false, the whole question is invalid.

So now MacLatchie revisits the debate, and what does he do? He just reiterates his flawed premises!

For those who want the bottom line, here it is. Myers thinks I’m worried about Haeckelian recapitulation. But that’s completely wrong. Neo-Darwinism itself predicts that early development, starting with fertilization, should be conserved.

And then just to make himself look even more stupid, he restates it in simple-minded logical terms.

The logic of my position takes a modus tollendo tollens form of argument:


1 If P then Q
2 ~ Q
3 ~ P

By instantiation in A


1 If the theory of common descent is true then early developmental stages should be conserved.
2 Early developmental stages are not conserved.
3 The theory of common descent is not true.

The argument is impeccable: Whence the disagreement?

And as if that were not enough, he closes his post by reiterating a variation of the same argument:


1 If the theory of common descent is true then mutations to early developmental stages should be beneficial.
2 Early developmental mutations are not beneficial.
3 The theory of common descent is not true.

Good god. After I lectured him about how early developmental stages are not conserved, after I wrote the same thing, after I posted a refutation of his claims by pointing out that his premise is false, he somehow thinks he can win me over by repeating his premises a little more loudly?

Let’s make this equally simple-minded and clear.

Neo-Darwinism does not predict that early development will be conserved.

If it did, since it is trivially observable that there is wide variation in the status of the embryo at fertilization, then neo-Darwinism would be refuted, and would have been falsified prior to its formulation. Yet somehow, people like me, like Pere Alberch who he cited last time and like Rudy Raff who he cites this time, have no problem with evolution while openly discussing the divergence in early embryos.

Think about that, MacLatchie. Isn’t it obvious that you must be missing something?

Here’s another counter-example: Ernst Mayr, about as authoritative a source as you can find on the neo-Darwinian synthesis, wrote a very negative assessment of the likelihood of any molecular homology in the 1960s, before lots of sequence information became available.

Much that has been learned about gene physiology makes it evident that the search for homologous genes is quite futile except in very close relatives (Dobzhansky 1955). If there is only one efficient solution for a certain functional demand, very different gene complexes will come up with the same solution, no matter how different the pathway by which it is achieved (Mayr 1966:609).

Mayr died in 2005, at a time when there was a wealth of comparative information on the ubiquity of conserved genes in development: not only wasn’t conservation of homologous developmental genes a prediction of evolutionary theory, but discovery that there were homologous sequences didn’t induce Mayr to recant evolution on his deathbed.

Is it sinking in yet?

Neo-Darwinism does not predict that early development will be conserved.

It is just freakin’ bizarre to see these guys falling all over themselves to declare that a specific prediction of evolutionary theory has been falsified, when they can’t even comprehend that it is the scientists studying the phenomenon who are handing them all the data that they think invalidates the scientists’ science. The closest thing I can find to it is those crazy creationists who claim that evolutionary theory requires junk DNA, so every time a minor function for any piece of DNA is found, they can claim evolution is refuted.

MacLatchie is hopelessly confused. That early stages should be more resistant to change is not a prediction of evolutionary theory; it’s an inference from molecular genetics, that genes at the base of a long chain of essential interactions ought to be less likely to vary between species. What that doesn’t take into account is that genes are part of the great cloud of environmental interactions that go on to generate a selectable function, and that if the environment in which the gene is expressed changes, it can enable great changes in the activity of the gene.

These early genes are a classic example of this phenomenon: what we see in many lineages is variation in the degree of maternal investment in the egg. It can be yolky, it can be low in yolk, it can have cytoplasmic determinants directly imbedded by maternal factors in the egg, or it can be mostly uniform and regulative. The early zygotic genes can be freed up for evolutionary novelties if their functions are assumed by maternal genes, so we can correlate a lot of this variation with variation in maternal investment.

It wouldn’t be a creationist paper without a quote mine, and MacLatchie does not fail: he quotes Rudolf Raff to support his claims. Rudolf Raff! One of the founders of the whole field of evo-devo! Dragooned into supposedly supporting an Intelligent Design creationism claim! These guys have no shame at all.

Unfortunately, I haven’t read the specific paper MacLatchie cites, but I’m familiar with the work: this is Raff’s beautiful examination of two closely related urchin species, Heliocidaris erythrogramma and H. tuberculata, which are practically indistinguishable in their adult morphology but have radically different embryos. Here’s the abstract, at least, from the paper MacLatchie chose to distort:

Larval forms are highly conserved in evolution, and phylogeneticists have used shared larval features to link disparate phyla. Despite long-term conservation, early development has in some cases evolved radically. Analysis of evolutionary change depends on identification of homologues, and this concept of descent with modification applies to embryo cells and territories as well. Difficulties arise because evolutionary changes in development can obscure homologies. Even more difficult, threshold effects can yield changes in process whereby apparently homologous features can arise from new precursors or pathways. We have observed phenomena of this type in closely related sea urchins that differ in developmental mode. A species developing via a complex feeding larva and its congener, which develops directly, have different embryonic cell lineages and divergent patterns of early development, but converge on the adult sea urchin body plan. Despite differences in embryonic developmental pathways, conserved gene expression territories are evident, as are territories whose homologies are in doubt. The highly derived development of the direct developer evidently arises from an interplay of novel organization of the egg, loss of expression of regulatory gene involved in production of feeding larval features, and changes in site and timing of expression of a number of genes.

I’ve highlighted the relevant part of the story for poor blind MacLatchie. One species is a direct developer: it lays a large yolk-rich egg which develops directly into the round spiky adult form. The other is an indirect developer, which lays a less yolky egg which first forms a feeding ciliated larva which swims about eating before making a metamorphosis into the adult form. These are radically different embryonic forms.

Gosh, I guess evolution is false.

But no! Remember, neo-Darwinism does not predict that early development will be conserved.

The explanation is given right there in Raff’s abstract, which MacLatchie must have read, and equally obviously must not have understood. Raff does, though: he understands that there were evolutionary changes in “novel organization of the egg, loss of expression of regulatory gene involved in production of feeding larval features, and changes in site and timing of expression of a number of genes,” all phenomena entirely compatible with evolutionary theory.

As one last instance of the muddled logic of Jonathan MacLatchie, I will leave you with two quotes from him. The first is from his last article on this subject:

At best, all his case demonstrated was common ancestry — a proposition which is perfectly compatible with intelligent design.

This is a common statement from creationists like Behe, who also say they have no problem with common descent, it’s just that they don’t accept that mutation and selection and natural processes could possibly have done the job. So MacLatchie is just stating the nominal, default, superficial position of many Intelligent Design creationists.

This time around, though, he says this:

If common descent is true, however, early development must somehow evolve via mutations.

Oh, really? Which is it going to be? Does he think common descent is true or not true?

He doesn’t need to answer, I already know it: whichever claim suits his current rhetorical purposes.

How could gay people evolve?

You can find a thorough explanation at Scientific American, which can be summarized by one simple phrase: Natural selection isn’t all-powerful. There are other complicating factors that Jeremy Yoder mentions as well — I might summarize that as “evolution is more complicated than you think.”

He did leave out a few important factors, though. One is pleiotropy; same-sex preference could be genetically coupled to some other attribute that offsets the hypothetical cost in reproduction. Another is that, well, I haven’t seen any good data to show that homosexuals actually have a reduced reproductive success. Historically, gay men and women’s desires haven’t mattered much when social pressures push you into a heterosexual marriage with the goal of producing children, and also, just being heterosexual does not imply that you will have lots of children. What people want and what people do haven’t necessarily been tightly linked.

The biggest additional factor to my mind is that it may not be heritable at all (I’m not dazzled by the evidence for a heritable component). Yoder mentions that it could be polygenic, but not that it could be environmental. This is not to say that it is non-biological, or worse, a matter of choice: we know that hormones can affect the developing embryo in interesting ways, and we also know the mind can be shaped in significant and irreversible ways by early experience. He has some nice charts that show if homosexuality were transmitted as a single allele, the simplest possible case, it would still persist in our population despite selection, but it may be a completely irrelevant model.

Jonathan MacLatchie collides with reality again

Jonathan MacLatchie, the creationist who challenged me to answer his questions about development in Glasgow, has posted his account of our encounter and his problems with evolution. It is completely unsurprising — he still doesn’t understand any of the points.

Of his 10 questions, 7 were quickly dismissable and were more than thoroughly addressed in my talk. They rest on a deep misconception that is shared with Jonathan Wells and many other pseudoscholarly creationists; I can summarize it with one standard template: “Since Darwinian evolution predicts that development will conserve the evolutionary history of an organism, how do you account for feature X which doesn’t fit that model?” To which I can simply reply, “Evolution does not predict that development will conserve the evolutionary history of an organism, therefore your question is stupid.” It doesn’t matter how many X’s he drags out, given that the premise is false, the whole question is invalid. But they can play that rhetorical game endlessly, citing feature after feature that doesn’t fit their misunderstanding of the science, making it sound to the clueless like they’ve got a legion of contradictions with evolution. Unfortunately for them, their objections are to creationist evolution, which has very little relationship to real evolution.

The gist of my talk was that Haeckel was wrong, that there was no recapitulation of developmental stages. Variation can and does occur at every stage of development; early and late stages vary greatly; evolution does not proceed primarily by terminal addition of new stages, as Haeckel postulated; but there is an interesting and real convergence on the broad, general outlines of the body plan at one point in development that needs to be explained.

MacLatchie’s response, greatly abbreviated, is to say that recapitulation doesn’t occur; variation occurs at every stage of development; early and late stages vary greatly; and look! I have papers from the peer-reviewed scientific literature that agree with me! Well, yes. That’s what I said. That is the conventional, ordinary, normal, well-understood, evolution-compatible side of the story from the scientists, like I’d been saying. Is there an echo in here, or do you just not understand what you heard or what you read, that you think the facts are evidence against evolution?

Apparently, in the Q&A for my talk (which you can now listen to; MacLatchie is first up), he asked me, I think, question #3 from his list, but I couldn’t really tell. As is typical, he turned it into a long-winded turgid mess, and I’ll be honest, I really couldn’t grasp what he was trying to ask, and I think he was actually getting at two different things. One is that there are differences in the embryological origins of some organs; this bothers him, apparently, because he’s sitting there expecting that there shouldn’t be any differences in how, for instance, the neural tube forms, because it’s a primitive structure, and therefore, because development is supposed to recapitulate evolution, they should be identical. I missed that; I was trying to see a more intelligent question in his verbiage. Now that I’ve read the papers he was waving around, I can answer a little differently: yes. There are differences in how different organs form in different species.


It is not a tenet of evo-devo that primitive structures must follow identical ontogenetic pathways. We actually understand that divergence can occur at all stages of development.

The other thing he was getting at was something I thought I understood when I tried to get him to focus on one example, and suggested neural tube formation. There what we see despite differences between species is a widely conserved molecular homology — that there is an interplay between BMP and Dpp in defining the prospective nervous system in flies and vertebrates. These deep homologies in organization were not expected and not predicted by evolutionary biology, but their presence does imply evolutionary affinities. That there are differences — for instance, a frog will form a hollow tube by folding the sheet of the neural plate, while a fish seems to submerge the sheet into the body and then secondarily cavitate* — are real, but relatively superficial. And differences are not precluded by evolutionary theory!

I wish I could get that one thought into these guys heads: evolutionary theory predicts differences as well as similarities. Finding a difference between two species does not send us rocking back on our heels, shocked that such a thing could be.

There’s another weird thing in that clip that is so typical of creationists. He pointed at those papers of his, dropped a few scientists’ names, and claimed they all supported his position. They do not. He gave me copies of three of them afterwards; two I’d already read and was fairly familiar with. Come on, he was citing Pere Alberch, the great synthesizer of development and evolution, in support of intelligent design creationism?

MacLatchie doesn’t even understand the paper. What Alberch is doing in it is arguing that many efforts to use developmental information in systematics go wrong because they have a creeping Haeckelian interpretation, that the sequences of events in development should preserve the evolutionary sequence. They don’t, he said, and as I also said, Haeckelian recapitulation is false. So, once again, MacLatchie was confronting me with a paper that confirmed what I had said as if it somehow showed I was wrong. I really don’t get it.

It’s also a subtle example of quote-mining. In the paper, Alberch gives two examples of developmental variation in vertebrates, describing differences in toe number and in the mode of neural tube formation. MacLatchie quotes him this way:

According to the Alberch paper (the claims of which remain true to this day), it is noted that it is “the rule rather than the exception” that “homologous structures form from distinctly dissimilar initial states.”

First, it’s a slightly odd quote: the two phrases are from two different paragraphs, and are in the reverse order from how they’re written here. He doesn’t substantially change the meaning, though, so it’s not quite as nasty as the usual scrambling. (However, it is peculiar that this same exact cut & flip quote can also be found in the works of Harun Yahya, and who knows where he got it; it’s just another example of creationists copying each other.)

However, this is where it gets devious. MacLatchie omits to mention the very next sentence after part of that quote:

The diversity of tarsal morphology, as well as the variation in ontogenetic pathways leading to the formation of the neural tube, reflect variations in developmental parameters or initial conditions within conserved developmental programs. [emphasis mine] There is structural organization in this scheme that should be amenable to systematic analysis but the information in not in the ontogenetic sequence.

You see, that’s the point of his paper: it’s a criticism of naive interpretations of developmental processes that are built on Haeckelian assumptions that the sequence of stages will be evolutionarily conserved. They aren’t. This does not represent a denial of evolutionary relevance; quite the contrary, he goes on to propose better ways of examining the role of development. After giving some examples, he explains that better methods “share the common emphasis on regulation within a resilient developmental program, and they emphasize the need to go beyond the perception of ontogeny as a sequence of discrete developmental stages.”

It’s actually surprisingly offensive to see creationist citing the late Alberch as somehow supporting their lunatic views. I suddenly feel like I was not rude enough to MacLatchie at that talk.

It’s a superficial ploy creationists play. They don’t have any scientific literature of their own, so they go rummaging about in the genuine scientific literature and start pulling out fragments that show disagreement and questions in the evolutionary community. And that is so trivial to do, because they don’t grasp something obvious and fundamental: every science paper has as its throbbing heart a question and an argument. Seriously. Every single paper on evolution is arguing with evolution, probing and pushing and testing. I am not at all impressed when some clueless dingbat pulls up Alberch’s paper titled “Problems with the interpretation of developmental sequences” and crows about finding a paper that talks about “problems”. Problems are what we’re interested in.

In an attempt at turnabout, MacLatchie also tries to claim that I distorted Jonathan Wells’ position by implying that Wells does not try to use Haeckel’s errors to undermine the foundations of evolution, because Wells openly explains that Haeckel was discredited by his peers.

A casual reading of chapter 3 of Wells’ The Politically Incorrect Guide to Darwinism and Intelligent Design (which was cited by Myers) reveals that Wells, in fact, tells us that “Haekel’s fakery was exposed by his own contemporaries, who accused him of fraud, and it has been periodically re-exposed ever since.”

Why, yes, it’s part of Wells’ game. He declares that Haeckel’s theory has been thoroughly rubbished, and therefore the foundations of ‘Darwinism’ have been destroyed. Note the sneaky substitution: Haeckel’s theory is not the foundation of evolution. We can kill it, kick it when it’s down, run it through a woodchipper, and it just doesn’t matter — it’s not part of evolutionary theory. I’ve dealt with this subterfuge at length, so I don’t really need to go into it again, do I?

*Which has since been found to be less of a difference than thought before. The fish neural tube does fold, but the cells are more tightly adherent to one another so you don’t see the central ventricle forming as obviously.

I said 7 of the 10 questions are blown to smithereens by the simple fact that they are built on false premises — MacLatchie doesn’t really understand that Haeckelian recapitulation is not part of evolutionary theory. I’ll quickly answer the remaining three right here.

4) Could you please explain the near-total absence of evidence for evolutionarily relevant (i.e. stably heritable) large-scale variations in animal form, as required by common descent? “Near-total”, that is, because losses of structure are often possible. But common descent requires the generation of anatomical novelty. Why is it the case that all observed developmental mutations that might lead to macroevolution (besides the loss of an unused structure) are harmful or fatal?

This is just like the standard creationist claim that there are no transitional fossils: there are no transitional mutations, either! When we see variations in morphology between populations of organisms, how did those changes get there, were they implanted by angels? As clear examples of “transitional mutations”, I’d point to polyphenisms, cases where there are discrete differences between genetically identical individuals based entirely on their environment.

I also suspect that the poorly explained basis of his question is that lab-generated mutations tend to be changes of very large effect on single genes. Polygenic phenomena are much harder to pick up and harder to analyze, and subtle variations in a fly or a worm are hard for us humans to detect, so the reason we see big, harmful mutations in the lab is because we’re looking for big, harmful mutations.

One more thing: look at sticklebacks. We find gross variations in form, armor, and spines that are caused by tiny changes in gene regulation.

8 ) On your blog, you have defended the central dogmatist (gene-centric) view that an organism’s DNA sequence contains both the necessary and sufficient information needed to actualise an embryo’s final morphology. If your position is so well supported and the position espoused by Jonathan Wells (and others) is so easily refuted, then why do you perpetually misrepresent his views? For example, you state “These experiments emphatically do not demonstrate that DNA does not matter … [Wells’] claim is complete bunk.” Where has Jonathan Wells stated that DNA “does not matter”? Moreover, contrary to your assertions, the phenomenon of genomic equivalence is a substantial challenge to the simplistic “DNA-is-the-whole-show” view espoused by the majority of neo-Darwinists. Cells in the prospective head region of an organism contain the same DNA as cells in the prospective tail region. Yet head cells must turn on different genes from tail cells, and they “know” which genes to turn on because they receive information about their spatial location from outside themselves — and thus, obviously, from outside their DNA. So an essential part of the ontogenetic program cannot be in the organism’s DNA, a fact that conflicts with the DNA-centrism of neo-Darwinism. Some attempts to salvage DNA programs (e.g. Rinn et al.) rely on “target sequences” — molecular zipcodes, if you will — of amino acids that direct proteins to particular locations in the cell. But such “molecular zipcodes” do not create a spatial co-ordinate system, they presuppose it.

This one is totally hilarious. First sentence: he claims I advocate a central dogmatist (gene-centric) view that an organism’s DNA sequence contains both the necessary and sufficient information needed to actualise an embryo’s final morphology, and to support that, links to one of my articles where I supposedly get all totalitarian for dogmatic genecentrism. Go ahead, follow the link. I say exactly the opposite.

10) Why do Darwinists continue to use the supposed circuitous route taken by the vas deferens from the testes as an argument for common descent when, in fact, the route is not circuitous at all? The testes develop from a structure called the genital ridge (the same structure from which the ovaries develop in females, which is in close proximity to where the kidneys develop). The gubernaculum testis serves as a cord which connects the testes to the scrotum. As the fetus grows, the gubernaculum testis does not, and so the testis is pulled downward, eventually through the body wall and into the scrotum. The lengthening vas deferens simply follows. And, moreover, before the vas deferens joins the urethra, there needs to be a place where the seminal vesicle can add its contents.

Wait, what? The route isn’t circuitous? I don’t know about you, but my testicles dangle down right next to my penis, yet the plumbing connecting them has to go back up into my torso, then down and around to exit in just the right place, a few inches away. And yes, there has to be a fluid contribution from the prostate, but again, that organ is tucked away inside, away from the action. And why do the testes have to be dangling anyway? Put ’em up next to the prostate. It would make far more sense.

Sure, you can put together physiological explanations for why each of those organs is in its particular place, but it doesn’t change the fact that the whole assemblage is a contingent kluge stuck together opportunistically.

My talk at Glasgow Skeptics

Hey, it’s on youtube already. There may be a few moments where I look a bit strained — that’s because the video projector wasn’t working well, and we actually had it sitting on the floor kind of crookedly aimed at the screen, and a helpful fellow was maneuvering it to make sure the part I was referring to was on the screen rather than the wall or the ceiling. But fortunately for you, those clever folks who produced the video spliced my slides directly into the video.

It’s all about the real history of Haeckelian recapitulation and why evolution doesn’t predict the crazy stupid things creationists say it does and why Jonathan Wells is a perfidious dorkwad.