The greatest science paper ever published in the history of humankind

That’s not hyperbole. I really mean it. How else could I react when I open up the latest issue of Bioessays, and see this: Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules. Just from the title alone, I’m immediately launched into my happy place: sitting on a rocky beach on the Pacific Northwest coast, enjoying the sea breeze while the my wife serves me a big platter of bacon, and the cannula in my hypothalamus slowly drips a potent cocktail of cocain and ecstasy direct into my pleasure centers…and there’s pie for dessert. It’s like the authors know me and sat down to concoct a title where every word would push my buttons.

The content is pretty good, too. It’s not perfect; the development part is a little thin, consisting mainly of basic comparative embryology of body plans, with nothing at all really about deployment of and interactions between significant developmental genes. But that’s OK. It’s in the nature of the Greatest Science Papers Ever Written that stuff will have to be revised and some will be shown wrong next month, and next year there will be more Greatest Science Papers Ever Written — it’s part of the dynamic. But I’ll let it be known, now that apparently the scientific community is aware of my obsessions and is pandering to them, that the next instantiation needs more developmental epistasis and some in situs.

This paper, though, is a nice summary of the emerging picture of cephalopod evolution, as determined by the disciplines of paleontology, comparative embryology, and molecular phylogenetics, and that summary is internally consistent and is generating a good rough outline of the story. And here is that story, as determined by a combination of fossils, molecular evidence, and comparative anatomy and embryology.

Cephalopods evolved from monoplacophoran-like ancestors in the Cambrian, about 530 million years ago. Monoplacophorans are simple, limpet-like molluscs; they crawl about on the bottom of the ocean under a cap-like shell, foraging snail-like on a muscular foot. The early cephalopods modified this body plan to rise up off the bottom and become more active: the flattened shell elongated to become a cone-like structure, housing chambers for bouyancy. Movement was no longer by creeping, but used muscular contractions through a siphon to propel the animal horizontally. Freed from its locomotor function, the foot expanded into manipulating tentacles.


These early cephalopods, which have shells common in the fossil record, would have spent their lives bobbing vertically in the water column, bouyed by their shells, and with their tentacles dangling downward to capture prey. They wouldn’t have been particularly mobile — that form of a cone hanging vertically in the water isn’t particularly well-streamlined for horizontal motion — so the next big innovation was a rotation of the body axis, swiveling the body axis 90° to turn a cone into a torpedo. There is evidence that many species did this independently.

The tilting of the body axes of extant cephalopods. This was a result of a polyphyletic and repeated trend towards enhanced manoeuverability. The morphological body axes (anterior-posterior, dorso-ventral) are tilted perpendicularly against functional axes in the transition towards extant cephalopods.

We can still see vestiges of this rotation in cephalopod embryology. If you look at early embryos of cephalopods (at the bottom of the diagram below), you see the same pattern: they are roughly disc-shaped, with a shell gland on top and a ring of tentacle buds on the bottom. They subsequently extend and elongage along the embryonic dorsal-ventral axis, which becomes the anterior-posterior axis in the adult.

In extant cephalopods the body axes of the adult stages are tilted perpendicularly versus embryonic stages. As a con- sequence, the morphological anterior-posterior body axis between mouth and anus and the dorso-ventral axis, which is marked by a dorsal shell field, is tilted 908 in the vertical direction in the adult cephalopod. Median section of A: Nautilus, B: Sepia showing the relative position of major organs (Drawings by Brian Roach). C: shared embryonic features in embryos of Nautilus (Nautiloidea) and Idiosepius (Coleoidea) (simplified from Shigeno et al. 2008 [23] Fig. 8). Orientation of the morphological body axes is marked with a compass icon (a, anterior; d, dorsal; p, posterior; v, ventral; dgl, digestive gland; gon, gonad; ngl, nidamental gland).

The next division of the cephalopods occurred in the Silurian/Devonian, about 416 million years ago, and it involved those shells. Shells are great armor, and in the cephalopods were also an organ of bouyancy, but they also greatly limit mobility. At that early Devonian boundary, we see the split into the two groups of extant cephalopods. Some retained the armored shells; those are the nautiloids. Others reduced the shell, internalizing it or even getting rid of it altogether; those are the coleoids, the most successful modern group, which includes the squids, cuttlefish, and octopuses. Presumably, one of the driving forces behind the evolution of the coleoids was competition from that other group of big metazoans, the fish.

The nautiloids…well, the nautiloids weren’t so successful, evolutionarily speaking. Only one genus, Nautilus has survived to the modern day, and all the others followed the stem-group cephalopods into extinction.

The coleoids, on the other hand, have done relatively well. The number of species have fluctuated over time, but currently there are about 800 known species, which is respectable. The fish have clearly done better, with about 30,000 extant species, but that could change — there are signs that cephalopods have been thriving a little better recently in an era of global warming and acute overfishing, so we humans may have been giving mobile molluscs a bit of a tentacle up in the long evolutionary competition.

There was another major event in coleoid history. During the Permian, about 276 million years ago, there was a major radiation event, with many new species flourishing. In particular, there was another split: between the Decabrachia, the ten-armed familiar squid, and the Vampyropoda, a group that includes the eight-armed octopus, the cirroctopodes, and Vampyroteuthis infernalis. The Vampyropoda have had another locomotor shift, away from rapid jet-propelled movement to emphasizing their fins for movement, or in the case of the benthic octopus, increasing their flexibility to allow movement through complex environments like the rocky bottom.

Time for the big picture. Here’s the tree of cephalopod evolution, using dates derived from a combination of the available fossil evidence and primarily molecular clocks. The drawings illustrate the shell shape, or in the case of the coleoids, the shape of the internal shell, or gladius, if they have one.

A molecularly calibrated time-tree of cephalopod evolution. Nodes marked in blue are molecular divergence estimates (see methods in Supplemental Material). The divergence of Spirula from other decabrachiates are from Warnke et al. [43], the remaining divergences are from analyses presented in this paper. Bold lineages indicate the fossil record of extant lineages, stippled lines are tentative relationships between modern coleoids, partly based on previous studies [41, 76, 82] and fossil relationships are based on current consensus and hypoth- eses presented herein. Shells of stem group cephalopods and Spirula in lateral view with functional anterior left. Shells of coleoids in ventral view with anterior down. The Mesozoic divergence of coleoids is relatively poorly resolved compared to the rapid evolution of Cambro- Ordovician stem group cephalopods. Many stem group cephalopod orders not discussed in the text are excluded from the diagram.

The story and the multiple lines of evidence hang together beautifully to make a robust picture of cephalopod evolution. The authors do mention one exception: Nectocaris. Nectocaris is a Cambrian organism that looks a bit like a two-tentacled, finned squid, which doesn’t fit at all into this view of coleoids evolving relatively late. The authors looked at it carefully, and invest a substantial part of the review discussing this problematic species, and decided on the basis of the morphology of its gut and of the putative siphon that there is simply no way the little beast could be ancestral to any cephalopods: it’s a distantly related lophotrochozoan with some morphological convergence. It’s internal bits simply aren’t oriented in the same way as would fit the cephalopod body plan.

So that’s the state of cephalopod evolution today. I shall be looking forward to the Next Great Paper, and in particular, I want to see more about the molecular biology of tentacles — that’s where the insights about the transition from monoplacophoran to cephalopod will come from, I suspect.

Kröger B, Vinther J, Fuchs D (2011) Cephalopod origin and evolution: A congruent picture emerging from fossils, development and molecules: Extant cephalopods are younger than previously realised and were under major selection to become agile, shell-less predators. Bioessays doi: 10.1002/bies.201100001.

A little cis story

I found a recent paper in Nature fascinating, but why is hard to describe — you need to understand a fair amount of general molecular biology and development to see what’s interesting about it. So those of you who already do may be a little bored with this explanation, because I’ve got to build it up slowly and hope I don’t lose everyone else along the way. Patience! If you’re a real smartie-pants, just jump ahead and read the original paper in Nature.

A little general background.


Let’s begin with an abstract map of a small piece of a strand of DNA. This is a region of fly DNA that encodes a gene called svb/ovo (I’ll explain what that is in a moment). In this map, the transcribed portions of the DNA are shown as gray shaded blocks; what that means is that an enzyme called polymerase will bind to the DNA at the start of those blocks and make a copy in the form of RNA, which will then enter the cytoplasm of the cell and be translated into a protein, which does some work in the activities of that cell. So svb/ovo is a small piece of DNA which, in the normal course of events, will make a protein.

Most of the DNA here is not transcribed. Much of it is junk — changing the sequence of those areas has no effect on the protein, and has no effect on the appearance or function of the organism. Some of it, though, is regulatory DNA, and its sequence does matter. The white boxes labeled DG2, DG3, Z, A, E, and 7 are regions called enhancers — they are not translated into protein, but their sequence affects the expression of svb/ovo. One way to think of them is that they are small parking spots for other proteins that will bind to the DNA sequences in each enhancer. These protein/DNA complexes will then fold around to make a little landing zone for the polymerase, to encourage transcription of the svb/ovo gene. This is why this is called regulatory DNA: it doesn’t actually make the svb/ovo protein itself, but it’s important in controlling when and where and how much of the svb/ovo protein will be made.

Now for some jargon; sorry, but you have to know what it is to follow along in the literature. Those little white boxes of regulatory DNA are often called cis factors, because they have to be located on the same strand of DNA as the protein-coding gene in order to work. In general, when we’re talking about cis factors, we’re talking about non-coding regulatory DNA. The complement of that is the actual coding sequence, the little gray boxes in the diagram, and those have the general name of trans factors.

There is a bit of a debate going on about the relative importance of cis and trans mutations in evolution. Proponents of the cis perspective like to point out that cis mutations can be wonderfully subtle and specific; you can make a change in an enhancer and only modify the expression of the gene in one tissue, or even a small part of one tissue, while changing a trans factor causes changes in every tissue that uses that gene product. Also, most of the cis proponents are evo-devo people, scientists who study the small variations in timing and magnitude of gene expression that lead to differences in form, so of course the kinds of changes that affect the stuff we study must be the most important.

Proponents of the trans view can point out that small changes in the coding regions of genes can also produce subtle shifts in what the genes do, and that mutations can also produce very large effects. Those cis changes appear to be little tweaks, while trans changes can run the gamut from non-existent/weak to strong, and so have great power. They also like to point out that most of the data in the literature documents trans changes between species, and that a lot of the evo-devo stuff is speculative.

It’s a somewhat silly debate, because we all know that both cis and trans effects are going to be found important in evolution, in different ways in different organisms, and that arguing about which is more important is kind of pointless — it will depend on which feature and which species you’re looking at. But the debate is also useful as a goad to urge people to look more at the subtleties and ask more questions about those enhancers, as in the paper I’m about to describe.

What is this svb/ovo gene?


This is a drawing of just the back end of a fly larva, and what you should be able to see is that they’re very hairy. Dorsally, there’s a collection of small hairs called trichomes, and ventrally there are some thicker, stouter hairs called denticles. If you destroy the svb/ovo coding region, these hairs don’t form — svb is an important gene for organizing and making hairs on the cuticle of the fly. It’s name should make sense: svb is short for shavenbaby. The gene is responsible for making hairs, but when you break it with a mutation you get embryos and larvae lacking those hairs, a shaven baby.

It also has the synonym of ovo, because it has another important function in the maturation of oocytes, something I’ll skip over entirely. All you need to know is that svb/ovo is actually a large complex gene with multiple functions, and all we care about right now is its function of inducing hair development.

Now let’s look at embryos of two different species of fruit flies, Drosophila melanogaster at the top, and Drosophila sechellia at the bottom. D. melanogaster is clearly hairier than D. sechellia, and you might be wondering if svb is the gene making a difference here, and if you’re following the debate, you might be wondering whether this is a change in the trans coding region or the cis regulatory region.


One way to figure this out is to sequence and compare maps of the svb region in multiple fly species and ask where the actual molecular differences are. This isn’t trivial: D. melanogaster and D. sechellia have been diverging for half a million years, and there have been lots of little changes all over the place, many of them expected to be neutral. What was done to narrow the search was to compare the sequences of five different Drosophila species with hairy embryos to the relatively naked D. sechellia, and ask which changes were unique to the less hairy form.

A hotspot lit up in the comparison: there is one region, about 500 base pairs long, in the enhancer labeled “E” in the diagram at the top of the page, which contained 13 substitutions and one deletion unique to D. sechellia, in 7 clusters. This is very suggestive, but not definitive; these are consistent differences, but we don’t know yet whether these molecular differences cause the differences in hairiness. For that, we need an experiment.

The experiment.

This is the cool part. The investigators built constructs containing the E enhancer coupled to the svb gene and a reporter tag, and inserted those into fly embryos and asked how they affected expression; so they could effectively put the D. sechellia enhancer into D. melanogaster, and the D. melanogaster enhancer into D. sechellia, and ask if they were sufficient to drive the species-specific pattern of svb expression. The answer is yes, mostly: they weren’t perfect copies of each other, suggesting that there are other elements that contribute to the pattern, but the D. sechellia enhancer produced reduced expression in whatever fly carried it, while the D. melanogaster enhancer produced greater expression.

But wait, there’s more! The species differences were caused by differences in 7 clusters within the E enhancer. The authors built constructs in which the mutations in each of the 7 clusters was uniquely and independently inserted, so they could test each mutational change one by one. The answer here was that each of the seven mutations that led to the D. sechellia pattern had a similar effect, reducing very slightly the level of svb expression. Furthermore, they had a synergistic effect: the reduction in hairs when all 7 mutations were present was not simply the sum of the individual effects of each mutation alone.

What does it all mean?

One conclusion of this work is that here is one more clear example of a significant morphological difference between species that was generated by molecular modification of cis regulatory elements. Hooray, one more data point in the cis/trans debate!

Another interesting observation is that this is a phenotype that was built up gradually, by a set of small changes to an enhancer element. D. sechellia gradually lost its trichome hairs by the accumulation of single-nucleotide changes in regulatory DNA, each of which contributed to the phenotype — a very Darwinian pattern of change.

By modifying the regulatory elements, evolution can generate distinct, focused variations. Knocking out the entirety of the svb gene is disastrous, not only removing hairs but also seriously affecting fertility. The little tweaks provided by changes to the enhancer region mean that morphology can be fine-tuned by chance and selection, without compromising essential functions like reproduction. In the case of these two species of flies, D. sechellia can have a functional reproductive system, the full machinery to make functional hairs, but at the same time can turn off dorsal trichomes while retaining ventral denticles.

It all fits with the idea that fundamental aspects of basic morphology are going to be defined, not by the raw materials used to build them, but by the regulation of timing and quantity of those gene products — that the rules of development are defined by the regulatory activity of genes, not entirely by the coding sequences themselves.

Frankel N, Erezyilmaz DF, McGregor AP, Wang S, Payre F, Stern DL (2011) Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature 474(7353):598-603.

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.

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.

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.

Making faces

Faces are weird. They really are largely accidents of development — all the fine features that we consider lovely sculpted signifiers of beauty are really just products of developmental processes, and what we recognize as pretty is actually just a good job of assembly. I’ve been talking about this bizarre way the human face is built for many years, especially since my interest in teratology means I spend a fair bit of time looking at cases where the assembly goes drastically wrong (in fish, not people; I can make things go wrong in fish embryos in ways that would send the mob after me with torches and pitchforks if I did them to human babies). Here’s what your face looked like, once upon a time.

Drawings of the developing human head and face between the 4th and 5th week (adapted from Nelson, 1953). The top row are side views, and the bottom row are face views of the same stages. The face develops from extensions and fusions of the pharyngeal arches, structures which are found in all other vertebrates, and which are modified in different ways in different species. Abbreviations: m, maxillary process (upper jaw); j, lower jaw; h, hyoid; n, nasal pit.

See what I mean by weird? Embryonically, much of your face was constructed from these plastic bars of tissue called pharyngeal arches, which extend to meet at the midline and then fuse and shift in complicated ways to form the familiar face we see in the mirror.

Now, even better, the BBC has created a simulated time-lapse video of face assembly. There are patent rules to how these tissues move, and common birth defects, like cleft palate, are a consequence of simply understood errors in how these tissues come together in the midline.

The article makes the point that the characteristics of facial development are also relics of our fishy ancestors. I guess it’s a good thing I study these phenomena in fish, after all, in addition to benefit of not enraging the local peasantry.

The basics of building a kidney

I’m a major fan of kidneys — they’re fascinating organs for discussion of both development and evolution. Today I lectured about them in my human physiology course, but I could only briefly touch on their development, and instead had to talk on and on about countercurrent multipliers and juxtamedulary nephrons and transport membranes and all that functional physiology stuff. So I thought I’d get the evo-devo out of my system with a few words about them here.

Our kidneys go through an elaborate series of three major developmental stages — we essentially build three pairs of kidneys as embryos, and jettison two pairs as we go along. It actually looks like something out of Haeckel’s recapitulation theory, as we progressively assemble and then discard ‘primitive’ kidneys.


The first stage is the formation of the pronephric kidney. In the embryo, the circulatory system forms glomeruli, or tangled capillary beds, adjacent to the membrane that surrounds the body cavity, or coelom. Filtered plasma oozes into the coelom, and the pronephric kidney has ciliated openings into the coelom called nephrostomes, and the fluid is drawn into the tubules, where membrane pumps recover nutrients and salts and return them to the circulatory system. Whatever is left behind — wastes and water — trickles into the pronephric duct, which terminates in the cloaca.

It’s a simple, low pressure system that is adequate for collecting waste products from the early embryo. It relies on an existing cavity for collecting filtered fluids, and you can tell that it doesn’t use a high-pressure filtration scheme since it can get by with simple ciliary beating to cause fluid flow. It’s a primitive system that is retained for functional reasons: metabolizing embryonic cells are producing chemical waste products, and some kind of waste disposal system is essential for even this early stage.


The second stage is the mesonephric kidney. New tubules bud off the pronephric duct, but unlike the pronephric tubules, these are directly invested with capillary glomeruli and form spherical filtrate collectors called Bowman’s capsules. This is the big functional difference from the pronephros: filtered fluids are no longer collected indirectly from the coelom, but straight from the circulatory system. Some of the mesonephric tubules may retain a connection with the coelom, but this is no longer the sole way to collect filtrate.

The pronephros degenerates completely as the mesonephros takes over its job. As it withers away, the mesonephric tubules continue to use the pronephric duct, which gets renamed: it’s now called either the mesonephric duct, or if you prefer the old school names, the Wolffian duct. Even the mesonephros is doomed, though; it’s an intermediate stage that can cope with the light loads of waste produced by the embryo at this point, but an even more elaborate, more efficient kidney, the metanephros, is also beginning to grow, and it’s going to make the mesonephros superfluous.


The metanephric kidney, the third and final stage of development (the metanephric kidney is the familiar adult kidney we all possess), buds from the mesonephric duct and forms a unique structure with familiar elements. The new kidney makes branching ducts from a central collecting point, like a spray of flowers; these new ducts look just like mesonephric tubules, with a Bowman’s capsule on the outer, or cortical side of the kidney, and loops descending down into the medulla to generate a concentration gradient of salts used in generating hyperosmotic urine (which is what I talked about in class today, and won’t say anything further here). The subunits are similar to the mesonephric tubules, just arrayed in a different and specific organization for even more effective mechanisms for maintaining salt balance.

This metanephric stage is also complicated by the co-development of the reproductive system. The gonads are differentiating and forming alongside the degenerating mesonephric kidney. In addition, another duct, the Müllerian duct forms in parallel to the Wolffian duct, so now, briefly, we have two pairs of kidneys and two pairs of longitudinal ducts. This is going to be followed by consolidation and change, though, and it’s going to be a sex dependent pattern.

In females, the Wolffian duct is mostly going to degenerate and be lost, along with the mesonephros. The Müllerian duct is going to develop into the fallopian tubes, uterus, cervix, and upper vagina. The only part of the mesonephric duct retained will be the branch connecting the metanephros to the cloaca.

In males, the M&uum;llerian duct degenerates. Yes, it seems incredibly wasteful and pointless: we guys built this parallel duct as embryos, and then promptly threw it away, unused. Instead, the Wolffian/mesonephric duct is retained and becomes the ductus deferens, that useful tube for transporting sperm from the testis to the penis.

I think you can see what’s cool about the kidneys — they follow a sequential pattern of development that also happens to reflect the evolutionary history of kidneys. You might be tempted to speculate that it follows a Haeckelian model, where development necessarily follows an evolutionary trajectory because change can only come by addition of new features, but don’t be fooled. There are a couple of reasons why this peculiar pattern of retaining ancient kidney types is maintained.

One is existence of developmental linkages: disrupting any of these earlier kidneys leads to serious developmental anomalies in subsequent kidneys. Each kidney is built on the foundations of the previous one; mutations that would excise that old less efficient, less sophisticated form would also prevent the normal development of the metanephros. Even if they were totally non-functional, we would still need the patterning aspect of the primitive kidneys to be present.

The other reason is functional. The metanephric kidney is complex and intricate, and takes more time to develop — but cellular metabolism isn’t going to just stop everywhere else in the embryo and wait for the kidneys to be put in place. It’s like the situation when construction workers are building a house, and they still occasionally need to empty their bladders, even if the elaborate bathroom faced with Grecian marble and equipped with the latest German plumbing fixtures isn’t done yet … so a porta-potty is wheeled onto the site.

And that’s what I like about kidneys: all the funky relics of the construction process are still there, hanging out and seeming to contribute to an excessively complex tangle of complicated relationships.

Kalthoff K (2001) Analysis of biological development. McGraw-Hill, NY.