Limusaurus inextricabilis

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My previous repost was made to give the background on a recent discovery of Jurassic ceratosaur, Limusaurus inextricabilis, and what it tells us about digit evolution. Here’s Limusaurus—beautiful little beastie, isn’t it?

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Photograph (a) and line drawing (b) of IVPP V 15923. Arrows in a point to a nearly complete and fully articulated basal crocodyliform skeleton preserved next to IVPP V 15923 (scale bar, 5 cm). c, Histological section from the fibular shaft of Limusaurus inextricabilis (IVPP V 15924) under polarized light. Arrows denote growth lines used to age the specimen; HC refers to round haversian canals and EB to layers of endosteal bone. The specimen is inferred to represent a five-year-old individual and to be at a young adult ontogenetic stage, based on a combination of histological features including narrower outermost zones, dense haversian bone, extensive and multiple endosteal bone depositional events and absence of an external fundamental system. d, Close up of the gastroliths (scale bar, 2 cm). Abbreviations: cav, caudal vertebrae; cv, cervical vertebrae; dr, dorsal ribs; ga, gastroliths; lf, left femur; lfl, left forelimb; li, left ilium; lis, left ischium; lp, left pes; lpu, left pubis; lsc, left scapulocoracoid; lt, left tibiotarsus; md, mandible; rfl, right forelimb; ri, right ilium; rp, right pes; sk, skull.

What’s especially interesting about it is that it catches an evolutionary hypothesis in the act, and is another genuine transitional fossil. The hypothesis is about how fingers were modified over time to produce the patterns we see in dinosaurs and birds.

Birds have greatly reduced digits, but when we examine them embryologically, we can see precisely what has happened: they’ve lost the outermost digits, the thumb (I) and pinky (V), and retain the forefinger, middle finger, and ring finger (II-IV), which have been reduced and fused together. This is called Bilateral Digit Reduction, BDR, because they’ve lost digits from the medial and lateral sides, leaving the middle set intact.

Dinosaurs, when examined anatomically, seem to have a different pattern: they have a thumb (I), forefinger (II) and middle finger (III), and have lost the lateral two digits, the ring and pinky finger (IV-V). This arrangement has been advanced as evidence that birds did not evolve from dinosaurs, since they have different bones in their hands, and getting from one pattern to the other is complicated and difficult and very unlikely.

The alternative hypothesis is that there is no conflict, and that dinosaurs actually underwent BDR and their digits are II-III-IV…but that what has also happened is a frame shift in digit identities. So dinosaurs actually have three digits, which are the index, middle, and ring finger, but they’ve undergone a subtle shift in morphology so that their forefinger develops as a thumb, and so forth.

Now we could resolve all this easily if only the physicists would get to work and build that time machine so we could go back to the Mesozoic and study dinosaur embryology, but they’re too busy playing with strings and quanta and dark matter to do the important experiments, so we’ve got to settle for another plan: find intermediate forms in the fossil record. That’s where Limusaurus steps in.

Limusaurus has a thumb, a tiny vestigial nubbin, and has lost its pinky completely. This is a (I)-II-III-IV pattern, and is evidence of bilateral digit reduction in a basal ceratosaur. In addition, the forefinger has become very robust, and while still distinctly a digit II, has been caught in the early stages of a transformation into a saurian first digit. It’s evidence in support of the dinosaurian II-III-IV hypothesis and the frameshift in digit identity! It’s almost as good as having a time machine.

Want to learn more? Carl Zimmer has a summary of the digit changes, while one of the authors of the paper, David Hone, also discusses the digits (the story is a little more complicated than I’ve laid out), and also has more on the rest of the animal—it’s a herbivorous ceratosaur, which is interesting in itself.

Xu X, Clark JM, Mo J, Choiniere J, Forster CA, Erickson GM, Hone DWE, Sullivan C, Eberth DA, Nesbitt S, Zhao Q, Hernandez R, Jia C-k, Han F-l, Guo Y (2009) A Jurassic ceratosaur from China helps clarify avian digit homologies. Nature 459(18):940-944.

Digit numbering and limb development

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Answers in Genesis has evolutionary biology on the run now. In an article from 2002, Ostrich eggs break dino-to-bird theory, they explain that development shows that evolution is all wrong, since developmental pathways in different animals are completely different, and can’t possibly be the result of gradual transformations.

The first piece of evidence against evolution is the old avian digit problem. Birds couldn’t have evolved from dinosaurs, because they have the wrong finger order!

The research conclusively showed that only digits two, three and four (corresponding to our index, middle and ring fingers) develop in birds. This contrasts with dinosaur hands that developed from digits one, two and three. Feduccia pointed out:

‘This creates a new problem for those who insist that dinosaurs were ancestors of modern birds. How can a bird hand, for example, with digits two, three and four evolve from a dinosaur hand that has only digits one, two and three? That would be almost impossible.’

The second problem is that frogs and people develop hands in completely different ways, ways that are even more different than the order of the digits.

This is not the only example where superficially homologous structures actually develop in totally different ways. One of the most commonly argued proofs of evolution is the pentadactyl limb pattern, i.e. the five-digit limbs found in amphibians, reptiles, birds and mammals. However, they develop in a completely different manner in amphibians and the other groups. To illustrate, the human embryo develops a thickening on the limb tip called the AER (apical ectodermal ridge), then programmed cell death (apoptosis) divides the AER into five regions that then develop into digits (fingers and toes). By contrast, in frogs, the digits grow outwards from buds as cells divide (see diagram, right).

Dang. I might as well hang it up right now. There is no possible way around these intractable differences. Take me, Jesus, I have seen the ligh…oh, wait a minute. That isn’t right. It looks to me like Jonathan Sarfati is just hopelessly confused on the first problem (I can’t really blame him, though—it is a complicated issue that has been the subject of scientific arguments for two centuries), and is simply completely wrong on the second (and that one I do blame him for. Tsk, tsk.)

So first, let’s tackle the tricky problem, digit identity in evolution. Extend your right hand out in front of you, palm down. Your thumb should be sticking out towards the left, and by convention, that’s Digit I. Counting from left to right, your index finger is Digit II, middle finger is Digit III, ring finger is digit IV, and your pinky is Digit V. We have the primitive pentadactyl (five-fingered) hand, so figuring out who is who is fairly easy. The difficulties arise in species that have reduced the number of their digits—when they extend their three-fingered hand, we have to figure out which digits are missing before we assign numbers to the remaining fingers.

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One way is by looking at the adult anatomy. Looking at your hand, you probably notice that your thumb is quantitatively different from the other fingers: it only has two joints, instead of three. This is common, that Digit I has fewer phalanges, or segments, than the others, and this is the kind of property that allows anatomists to figure out whether Digit I is present or not. To the right, for instance, is the hand of the raptor Deinonychus (the left hand, sorry to confuse you) with its digit numbering, from DI to DII to DIII, an assignment that was made on the basis of the anatomy. You can see that the ‘thumb’, DI, has fewer phalanges than the others.

You can try to do the same thing with the digits of birds, but it’s harder. Avian digits are reduced and fused into that pointy thing you find at the end of a chicken wing, and it takes an expert to sort out what bones are blended together in there. Anatomists tried, though, and initially and long ago (Meckel came to this conclusion in 1825), decided the bones were numbered DI, DII, and DIII, just like the ones we see in three-fingered dinosaurs…so no dilemma, right?

Wrong. There’s another way of looking at the identity of these bones, and that is by watching them develop. What some birds do is start to make five fingers—they form four or five little nubbins of cartilage, called condensations, and then shut down the development of some of them. What another old time anatomist noticed (Owen, in 1836) was that one of the condensations that got thrown away was the first one—which means that the bird digits are actually derived from Condensation II, Condensation III, and Condensation IV. The data is even stronger in this day of molecular markers: bird digits arise embryonically from the second, third, and fourth cartilaginous condensations.

Now this is a complication for evolution. We have three-fingered dinosaurs, and three-fingered birds, but it looks like they aren’t the same fingers. Bird ancestors would have had to resurrect their discarded Digit IV, then eliminate Digit I, all before fusing the whole assemblage into a bony gemisch anyway. It’s not parsimonious at all. (Of course, it’s even less parsimonious to throw away more than a century of data supporting evolution, as Jonathan Sarfati would like us to do.)

There is another, better explanation that Wagner and Gauthier have made that clarifies everything to me, at least.

Note that anatomists initially assigned digit numbers I, II, and III to bird limbs on the basis of their form, but later had to revise that to II, III, and IV on the basis of embryology. Dinosaur digits are assigned numbers I, II, and III on the basis of their adult form (which is admittedly much less ambiguous than adult bird digits!)…but what about their embryology? If we had access to information about expression of molecular markers and early condensations in the dinosaur limb, would we have to revise their digit numbers?

We don’t have fetal dinosaur hands to experiment on, but our growing knowledge about how limbs develop suggests that that might just be the case. This diagram illustrates the sequence of development in the hand of an alligator (a) and an ostrich (b).

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What you’re seeing is the pattern of early condensations in the limb. We tetrapods have a standard pattern: the very first digit to develop as an extension of the limb is Condensation IV, your ring finger, forming what is called the metapterygial axis. Next, the pinky (CV) forms as a little afterthought along one side of the metapterygial axis, and a new axis of condensation hooks over the palm, with the middle finger (CIII) forming next, then the index finger (CII), and lastly the thumb (CI). From a developmental standpoint, the easiest digits to lose are that odd little CV, and the thumb, CI. CI is the very last to form, so you can stop its formation by changing the timing of development in a process called heterochrony, and just halting the development of that axis hooking across the palm early. You can see that in the ostrich, which just stops making fingers after CII, so CI doesn’t form. The hardest digit to lose is CIV, because it’s kind of the lynchpin of the process—all the other digits follow after IV, so it would be difficult to suppress IV without losing all of the other digits. (Who would have thought that the ring finger was so central and important to hand development?)

The numbering of the dinosaur limb is a problem then…it suggests that they don’t have a Digit IV, which looks like a complicated and unlikely thing to do. But they do have a ‘thumb’, or Digit I. How do we resolve this seeming contradiction?

The answer is that there are two developmental processes going on. The first is the formation of the condensations, CI through CV. This process partitions the terminal region into an appropriate number of chunks, but doesn’t actually specify the identity of the digits. The second process takes each of those chunks and assigns a digit identity to them, and this process is to some degree independent of the first and uses a different set of signals. Wolpert et al. have noticed this in modern embryos:

For example, digit identity is specified at a surprisingly late stage in limb development, and identity remains labile even when the digit primordia have formed. It now appears that digit identity is specified by the interdigital mesenchyme and requires BMP signaling. There is also evidence that mechanisms other than a diffusible morphogen operate to lay down the initial pattern of cartilage, which is then modified by a signal from the polarizing region…

What Wagner and Gauthier propose is that three-fingered dinosaurs accomplished that reduction by shedding the two easiest digits to lose, CI and CV, so that if we enumerated them by the same criteria we use in modern birds, they possess Condensations II, III, and IV. What also happened, though, was that there was a frame shift in the mechanism that assigns digit identity, so CII develops as DI, CIII as DII, and CIV as DIII.

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The timing of this shift can be mapped onto saurian phylogeny, and it all makes sense and is consistent. And it doesn’t involve taking seriously the silly sequence of the biblical account, which has birds appearing before all of the land animals.

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What about Sarfati’s second line of evidence against evolution, that frogs and humans use completely different mechanisms to build their limbs?

Simple answer: it’s all bullshit. It’s a blatant denial of basic information you’ll find in any developmental biology textbook.

We’ve got a pretty good handle on the outline of limb development in multiple tetrapod lineages now, and they all use the same tools. Contrary to Sarfati’s implication, they all have apical ectodermal ridges (with some rare exceptions in a few highly derived, direct-developing frogs) and zones of polarizing activity, they all use the same set of molecules, including FGF-4 and FGF-8 and the same Hox genes and retinoic acid and BMPs. If there’s one thing we know, it’s that limb development is dazzlingly well conserved.

It is true that frogs have less apoptosis between their digits than we do, but that’s because they have webbed feet. Suppress apoptosis in other vertebrates, and you get the same phenomenon, retention of membranous webs between the digits. There is a simple functional reason why they differ in this regard, and it takes advantage of a common property of limb development in all tetrapods.

I can sympathize with Sarfati having difficulty sorting out digit numbering—it’s subtle and sneaky and has puzzled smarter people than either of us. But the uninformed rejection of some of the most straightforward, clearest examples of common mechanisms in development, something that you can find described in the most introductory biology textbook…that’s hard to forgive.

Wagner GP, Gauthier JA (1999) 1,2,3=2,3,4: A solution to the problem of the homology of the digits in the avian hand. Proc. Natl. Acad. Sci. 96:5111-5116.

Wolpert L, Beddington R, Jessel T, Lawrence P, Meyerowitz E, Smith J (2002) Principles of Development. Oxford University Press.

A little sympathy for the snookered

As we all know to our great shame, Ken Ham has this Creation “Museum” in Kentucky. As has been reported before, it’s a thoroughly bogus bit of bunco, with dinosaurs wearing saddles and all the ills of the world laid at the feet of Charles Darwin.

There are a few things you might not know. Like that it’s rolling in dough, with almost $18 million in revenue and $14 million in assets. It’s entirely tax free, which helps, and Ham is a relentless self-promoter.

This one may shock you: public schools are sending kids on field trips to the museum. It’s usually under the guise of an extra-curricular activity by a religion club, the loophole David Paszkiewicz (remember him?) used to take kids from Kearny High School in New Jersey there. But get this remark from an education official in Kentucky:

Kentucky Department of Education spokeswoman Lisa Gross said nothing in state law would bar public schools from visiting, if it were part of “a lesson” on “how some perceived the world’s beginnings.”

You know Ham has friends in high places, and they are warming up to open his brand of nonsense and lies to the schools in that area. More minds, more souls, more money for Ken.

And of course, what is Ken Ham’s big, bold, explicit message? That the only tenable belief is in fundamentalist Christianity and a literal interpretation of Genesis. The crew at Answers in Genesis really detests theistic evolution — you know, that compromise position the accommodationists want us to bow down before. To these creationists, anything less than abject capitulation to Biblical literalism will lead to the collapse of Christian America.

Oh, but wait — I know what you are thinking. You’re thinking that this is insane. This is “stupid and crazy and wrong”. You might even be thinking, as I do, that this is dangerous and represents a corruption of education that is doing great harm to our country. You might also feel as I do, that we should not hold back in denouncing this blight of poisonous ignorance in our midst.

You’d be bad if you thought that.

Well, at least according to Michael Ruse, the Discovery Institute’s favorite evilutionist philosopher. You see, Ruse has recently visited the museum, as he wrote to Andrew Brown, and he tried to understand how the creationists feel.

Just for one moment about half way through the exhibit …I got that Kuhnian flash that it could all be true — it was only a flash (rather like thinking that Freudianism is true or that the Republicans are right on anything whatsoever) but it was interesting nevertheless to get a sense of how much sense this whole display and paradigm can make to people

Oh, right. Forget all that stuff about the earth being 6,000 years old, all the diversity of life on earth being packed into a boat for a year, and the adamant belief that atheists, agnostics, and theistic evolutionists are trying to destroy the nation for Satan…we’re supposed to feel for them, and try to understand their psychology. Ruse continues:

It is silly just to dismiss this stuff as false — that eating turds is good for you is [also] false but generally people don’t want to [whereas] a lot of people believe Creationism so we on the other side need to get a feeling not just for the ideas but for the psychology too.

This is what is so awful about the “New Atheists”: they are such horrible, insensitive louts. They can’t overlook the teeny tiny little demand of biblical literalism to see that creationism isn’t quite so wicked. That, at least, is what Andrew Brown dislikes about us.

This is, I think one of the key differences between the new, or militant, atheists and Darwinians like Ruse, just as atheist as they but a lot less anti-religious. The new atheists recoil instinctively from the idea that they should get a feeling for the ideas and psychology of creationists. To them the essential point about believers is that they are stupid and crazy and wrong. So why waste your one life trying to inhabit a mind smaller and more twisted than your own?

See? If only we’d try to see the world through their eyes, we would understand that their beliefs aren’t stupid and crazy and wrong. Or something. I’m not quite sure what. I guess we’re supposed to sympathize with them, and be less critical.

Well, guess what, Andrew and Michael? I do talk with creationists, and I do understand where they’re coming from, and I do sympathize with them greatly. Your assumption that I and other “New Atheists” do not care about the psychology of creationists is false, and I think, counter-productive.

I understand that many creationists are intelligent and sane — they share a lot of values with me, like wanting to be able to think as they please, to raise happy, healthy families, and they are very concerned about their children: they are sure that if their kids aren’t Christian, they’ll be miserable, wretched, and damned to hell for all eternity. I do sympathize with them. I feel great sympathy and sorrow for the fact that they’ve been lied to by deluded con men like Ken Ham, and that they’re living lives driven by an irrational fear…a fear that is reinforced every day by evangelists and fundamentalists and the whole petty shuck-and-jive of religious belief.

I sympathize with their kids, too. These are blameless innocents who are going to be brought up in ignorance, reassured constantly that their foolishness is a virtue, and that learning about this wonderful, beautiful, dangerous, and uncaring universe we live in will lead them to hell. No child should be brought up in fear and darkness.

I sympathize with their fate, because they’re going to grow up just like their parents and spread the fear and ignorance even further. They will want the best for their kids, too, and instead, under the guidance of pious liars, they will wreck those kids’ minds, too. And the cycle will go on and on.

I sympathize with all their secular neighbors most of all. What will happen? They will live in a country where their schools are third-rate, because the creationists will suppress education not just for their own kids, but for everyone else’s, too. They will see their school boards populated with the products of such fare as the Creation “Museum”, and they will get to vote in elections where their options are Insane-Fundie-Wackjob vs. Slightly-Less-Crazy-God-Botherer. And the lesser-of-two-evils won’t always win, because their neighbors all think the fundier, the better.

I sympathize because they are all missing the awesomeness of reality for the awfulness of some narrow Bronze Age theocratic bullshit.

But there are also some for whom I have no sympathy at all.

I have zero sympathy for intelligent people who stand before a grandiose monument to lies, an institution that is anti-scientific, anti-rational, and ultimately anti-human, in a place where children are being actively miseducated, an edifice dedicated to an abiding intellectual evil, and choose to complain about how those ghastly atheists are ruining everything.

Those people can just fuck off.

Give him a fair trial and then execute him!

The murder of George Tiller has brought some vile people creeping out from under the woodwork…especially the kinds of nasty minds that like to dress up in clerical collars. Looking for a good emetic? Look no further than this sermon by a Presbyterian minister for a great example of deploring a murder while praising the murderer’s motives.

A notorious murderer met what is certain to become a notorious end. By the goodness of God the witness of the Church was not entirely silenced in Dr. Tiller’s life. He had been excommunicated by his previous congregation, a church of the Missouri Synod Lutheran denomination. And so the judgment of God had been declared; not every watchman was silent, not every shepherd proved a hireling.

But the point was reached where a man despaired of change through government and took matters into his own hand. I do not view the actions of Dr. Tiller’s killer as defensible, but not for many of the easy and often self-serving reasons advanced with alarm and indignation even by many Christians in recent days.

  • Violence is not always wrong. Killing is not always forbidden. Opposition to abortion does not obligate us to oppose all forms of killing. In saying this I make a biblically defensible statement. God has given the power of the sword to the state so that it may judge and execute judgment. This is true internationally and locally. Condemnation of the vile sin of abortion, the murder of an infant, an innocent, in its mother’s womb is not the same as the death penalty, properly applied.

  • Nor do I believe that Dr. Tiller’s killer necessarily acted inappropriately as self-appointed judge, jury and executioner. Like the couple who boldly went into the tent before the congregation at Peor and were immediately killed by Phinehas, Dr. Tiller’s bold practice of the indefensible, his brazen boasting of his practice rendered judge and jury superfluous. He was self-accused and self-convicted.

But what Dr. Tiller’s killer did which Phinehas did not do was to kill against the will of the nation’s civil authority. It was an act of rebellion posing as an act of justice. The killer was an assassin who lacked the courage to attack the root of abortion, our national leaders, and so attacked the branch. His was not an act of saving babies or of executing justice. Other men will continue Dr. Tiller’s practice. A bucket of water taken from the sea will not create a hole in the ocean. Others will fill where Dr. Tiller left off. Abortion will proceed because, and this is vital to say, abortion is blessed by the law of the land. The logic of Dr. Tiller’s killer is the logic of John Brown, of Absalom, of Ehud.

Get that? It’s OK for anti-choicers to kill, and it is appropriate for them to execute abortion doctors, we just need to wait until the civil authorities declare it’s time to line them up against the wall. And Tiller’s murderer’s mistake was being insufficiently brave enough to attack the nation’s leaders.

I read the whole thing. Now I need to take a shower.

An ontogeny of toilet drain behavior

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I was recently sent a strange article for comment…well, not that recently. It’s 51 pages long, so I’ve kind of dragged my heels over it all. I have finally finished it, though, and it is weird.

There is a significant tradition in developmental biology that is currently a bit out of fashion: some names for it are formalism or structuralism. It’s the idea that forms arise from the application of simple physical properties to tissues, and that it would be possible to describe an organism in some way by a set of parameters plugged into a mathematical formula. It’s an interesting idea, it has a long history with some significant proponents (Goethe, for instance), and I’d even argue that there’s a solid kernel of truth to it — we should not ignore the importance of physico-chemical properties in shaping organisms! However, it’s an idea that has been eclipsed by the successes of molecular biology and genetics, which has moved the focus of research away from the general and universal, the fluid properties of membranes, for example, towards the particular and discrete, the actions of genes. A gene-centered research program has proven powerful, while the idea of exploring how global properties influence form…not so much.

I confess to a fair bit of sympathy for the idea that physical and chemical forces are significant, and that our current emphases in biology don’t do the concept justice. The best of the modern structuralists is, in my opinion, Brian Goodwin, and I find his work thought-provoking. No, more than that; he describes many processes that must be addressed from a structuralist position, and for which genes are inadequate descriptors. The giant in this field is, of course, D’Arcy Wentworth Thompson, whose classic work is On Growth and Form. It was written before genes, genes, genes took over biology, so it has a very different perspective from modern work; it’s also written in a wonderfully formal style that I find sublime but some may find a bit too old-fashioned. It would be required reading for all biologists, if I were the tyrant of the sciences. You’ll never look at a field of cells in quite the same way after reading it.

Unfortunately, structuralism also attracts more than its share of cranks. There’s something about reducing all the complexity of a mouse to an array of fields and vectors and mathematical formulae that draws in a certain kind of mind. It also sucks in a certain kind of person who doesn’t actually ever want to get his hands sticky and slimy poking around in a real live mouse, but wants the elegant purity of math — something he or she can do at a desk, where it’s clean and simple. Simplicity is also important to these people: all that fussy, nit-picky complexity of thousands of genes clutters their impeccably sterile mathematics. This means that the field is littered with kooks.

I reviewed a book of that sort from Stuart Pivar. It had all the characteristics of this genre: a shocking ignorance of actual biology, a weird obsession with a single physical cause (in his case, all organisms were toroids, or as I pointed out, balloon animals), and a willingness to ignore the petty problems of biology actually contradicting his conclusions.

This latest addition to the structuralist literature is a long paper by Vincent Fleury, called “Clarifying tetrapod embryogenesis, a physicist’s point of view”. It is nowhere near as crazy as Pivar’s work, so let’s get that out of the way — Fleury has at least read the developmental biology literature. Boy, has he read it — the bulk of his paper is a huge survey of introductory developmental biology. Part of the pain of reading the paper is that almost all of it is completely irrelevant to his thesis, and reading it from the point of view of a developmental biologist, it was too much like reading a smart undergraduate’s overlong term paper…a smart undergraduate who has decided that the appropriate subject is to attempt a complete overview of an entire field. This happens to me now and then; I try to catch it early, though, and steer the student into focusing on something manageable and specific. Too late for Fleury!

A voluminous overview of all of developmental biology (which, of course, fails — 50 pages is not enough!) is actually a distraction from making a point, unless perhaps that point is to flaunt some kind of misplaced erudition. So what is his point? Skip ahead to his last paragraph.

A possibility therefore appears, that the apparance[sic] of
tetrapods be generic, and that it follows a general law with few degrees of freedom, although it has lots of genetic parameters. In which case, Darwinian evolution plays with a very restricted set of shapes, with stringent internal (physical) correlations, and the known body forms might be unavoidable, in the long run.

This is not a very useful hypothesis. He’s basically saying that all tetrapods are four-limbed because there are physical constraints that stem from the earliest processes in the embryo that impose a general form on them. It’s rather tautological, for one thing, but it is also trivially true. I think all developmental biologists would agree that there are limits to the potential for morphological change in a lineage, but the question is the nature of the processes that impose the limits. Despite my sympathies for the structuralist idea, I’d have to say that what does that is the interlocking pattern of gene regulatory networks. Fleury wants to claim that it is hydrodynamics, and fluid flow, and shearing forces.

I don’t doubt that fluid properties are important in cell behavior, but the paper has only two modes of instruction: a long and somewhat pedantic description of known developmental genes (which does not advance his thesis at all), and another long section of hydrodynamic theory (which is not applied to any experimental or observational work in biology). There is no synthesis! The biology section is like an exercise in which the author shows off that he has done some homework, and the physics part is to demonstrate that he has the math to apply to problems of problems of fluid dynamics, but the two don’t meet. What I would want to see in order to be persuaded that this approach is viable would be a specific application of these principles of physics to a specific process in development, in either an experimental or comparative context. Show me how similarities and differences in form are better explained by differences in physical properties than by genetic differences (which then subsequently induce differences in physical properties).

The author is a physicist, and it shows. Not that I’m saying anything derogatory about physicists, but they have their own domain of expertise, while biologists have a different one, and I’m afraid you can’t just blindly assume expertise in one translates into the other, or I’d be designing rocketships right now. So many little things in this paper clued me in to the superficiality of Fleury’s knowledge of biology.

For example, and this is a very small thing that will grate on any biologist, is that he refers to single species as “specie”. The singular of species is “species”; specie is money in the form of coins. The third time Fleury did this, it was driving me nuts.

Then there’s this strangely indignant outburst.

True as well as extra limbs actually originate in the lateral
mesoderm of the flanks, in an area called “limb field” or
“lateral plate” or “limb plate”. While preparing this
review, I found it impossible to find a description of where
the lateral plates come from. All existing work assumes an
already formed lateral plate for the extension of the limb, or for the early expression of limb markers (such as Tbx5).

His confusion is utterly baffling: a two minute conversation with a generic, minimally experienced embryologist, like me, could have settled this easily enough. Cells invaginate in the embryo to form a mesodermal layer, a relatively undifferentiated sheet that progressively separates into paraxial and lateral plate mesoderm on the basis of their distance from the embryonic axis. It comes from the same place as the other mesoderm; it’s simply a sub-domain of the mesoderm that separates from the others.

It’s this kind of thing throughout the paper that gives the impression that his knowledge of the subject is an inch deep, and further, that he isn’t even willing to have a conversation with a biologist.

I’m very glad I wasn’t asked to formally review this paper, because it would have taken ages and would have required so much commentary that it would have been like writing a 50 page paper myself. Or maybe not: I would have short-circuited the whole thing by simply rejecting it outright and recommending that it might be worth re-evaluating after the author cut out 45 pages and distilled it down to some discriminating tests of his hypothesis.

Strangely, or perhaps not so strangely, the reviewers of this work did not do that. It’s a paper that was published in The European Physical Journal: Applied Physics! I am baffled again. Why it was accepted for a journal with such inappropriate content at all is a mystery, but at least we can presume that the reviewers were fellow physicists who were completely oblivious to the superficiality of the biology. Either that, or they were stunned by volume of basic biology shoveled up by the author, and signed off in surrender; anyone will confess to anything when waterboarded by that much introductory text.

All that aside, though, what ultimately kills the work is the maddening vagueness of its claims and implications. Here’s the pocket summary provided by the author.

Reviewing the paleontological, genetic, developmental and
physical data, shows that a dynamic picture of embryo
development, resting on fundamental laws of physics, can
be proposed. In this view, development consists in a continuum deformation of an initial formless animal which
progressively changes shape by scaling up an initial symmetry breaking. Starting from such a symmetry breaking,
a uniform behaviour of cells (constitutive equation) suffices to induce a deterministic asymptotic form, by low
Reynolds flow. The dimensionless flow forms a general
law, whose parameters have a genetic origin. Modifying
the parameters shifts the animal forms along morphological diagrams which follow the streamlines of the flow. Although several aspects (phaners, metabolism, cognition,
etc.) add to the problem lots of features which we have
not addressed, there may exist a simple biomechanical rationale that explains in detail the global pattern of embryo
structure in vertebrates. The formation of a streak, the invagination of the yolk-sac, the back and forth motion of
Hensen’s node, the formation of a body which has globally
the shape of “an 8”, the lateral position of the limb fields,
are all very complex and important developmental questions, which in fact may be reduced to simple hyperbolic
viscous flows in the embryonic sheets. These flows require
an initial symmetry breaking and possibly genetic pools of
molecules which overlap mechanical fields. The rationale
of animal formation is that of a cellular flow which runs
away by producing its own factors of self-organization.

An equation suffices to define form? Show me. Show me this “simple biochemical rationale that explains in detail the global pattern of embryo
structure in vertebrates,” because I don’t believe it is there, and it certainly isn’t shown in the paper. What hydrodynamic property makes a tetrapod different from an arthropod? Fleury doesn’t say. What differences in cellular flow make a squirrel different from a mouse? Fleury doesn’t say. Where are the measurements of forces in tissues in the gastrula that lead to the four-limbed state? Fleury doesn’t give them. What does this formula provide to developmental biologists that is not matched or vastly exceeded by the tools of molecular biology? Where are the successful, productive laboratory experiments we can carry out to test and extend this model? Fleury has nothing.

Where Pivar had toruses and drawings that reminded me of ballon animals, Fleury seems to believe development proceeds by swirling forces spinning about in the embryo, and gives us fictitious diagrams like this one.

i-6f5eb891d2b3a48308f24b9b477ec142-swirlyskull.jpeg
a drawing of an homo habilis skull, with a
pattern of presumptive stream lines superimposed. The head material rotates around the ear orifice (roughly), and above the
eye orbits.

Please show me cell movements or tensions in the developing skull that correspond in any way to those psychedelic lines. It’s completely nonsensical.

Swirl this one right down the drain, please.

Fleury, V (2009) Clarifying tetrapod embryogenesis, a physicist’s point of view. The European Physical Journal Applied Physics 45(3):30101.

Vincent Fleury has demanded the right to reply, and I’m always happy to help a fellow hang himself. Here’s what he sent me:

your review on my article in EPJ (Clarifying tetrapod embryogenesis)

was pointed to me by embarrased colleagues, who are appalled by such incompetence (I mean yours).

I am sorry to say that you understand very little physics.
It is not a big problem in so far as you do not make blatant deffamatory statements.

I am a bit choked by several statements which you make.

For example, I do give a hydrodynamic explanation of transiton from apes to humans.

I do give a hydrodynamic explanation of transition of lizards to snakes etc.
it is very easy from the examples I give to extrapolate to other cases.

I do show how equations may generate forms, it is so simple (moving boundary problems).

Your statement about the “psychedelic” image are really pathetic for you, since apparently not only you do not understand what a deformation rate field is, you are unable to follow basic rationales in the article, but you do not seem to be aware of the structure of the stress field in young heads (cephalic vesicle).

I certainly do not want to enter into a useless argument with you, but as a compensation for all the harm that your incompetent review will do, I would kindly request that you put side by side with the “psychedelic” image the animation which you will find in attachment with the caption “Animation showing the progressive deformation of a skull in a dipolar field of stretch, the animation concatenates a dipolar winding towards the past, and towards the future, of the skull in the <<psychedelic>> image”,
and a link to the pattern of shear lines in early brain vesicles :

http://www.msc.univ-paris-diderot.fr/~vincent/englishthemecerveau2.html

That will suffice to satisfy me, and you will certainly agree that it is not a big demand; I shall not go any further with you.

With my best regards

Vincent Fleury

Proof That God Exists?

That’s the title of the site, anyway, Proof That God Exists. It ain’t.

It’s a dreary exercise in the fallacy of the excluded middle. You are lead through a series of binary choices, in which you are asked to choose one alternative or the other, with the goal of shunting you to the desired conclusion, which is, of course, that God exists. Building on a fallacy is bad enough, but even worse, it can’t even do that competently — it cheats. All of the options are designed to bounce you to only one line of reasoning, and if you don’t play the designer’s game, it gets all pissy at you and announces that you aren’t serious and you should go away. Some proof, eh?

The one argument it channels you into is this one: there must be an absolute source of absolute morality, therefore, God. Francis Collins would be quite happy with it, I’m sure. When I took it, I agreed that there is an absolute truth (because I believe reality exists), I believe in logic and mathematics, but then when it asked if there is an absolute morality, I had to say no. Morality is a derived property generated by the interactions of individuals; it is not imposed on us from above. And that’s where the site gets nasty.

It gives you two choices: “Molesting children for fun is absolutely morally wrong” and “Molesting children for fun could be right”. If you answer the former, it bounces you back to the question about whether absolute moral laws exist…therefore God. You don’t get to choose something like “Molesting children is damaging to our species and harmful to individuals, and I agree with the cultural proscription against it”. If you answer the latter, you get their surrender message.

You have denied that absolute moral laws exist but you appeal to them all the time. You say that rape IS wrong because you know that it IS wrong and not just against your personal preference. Unless you reconsider your stand on this matter, your road to this site’s proof that God exists ends here. It is my prayer that you come to understand how inconsistent and irrational this line of thinking is and return to seek the truth.

I don’t think they understand the concept of a proof, or logic for that matter.

It is rather interesting that this is the most common “proof” people are throwing at us lately, this idea that the existence of a common morality in human cultures is evidence for a supreme being. It’s a sign of how weak and pathetic their arguments have become.

A Republican push-poll

The Republicans are asking the party faithful to fill out a biased poll. The purpose is not to get a snapshot of public opinion, but to mislead people by presenting leading questions. Or, as Mike Haubrich explains it:

The point of push-polling in politics is not to gather opinion, it is to “push” towards a certain viewpoint by exposing the opposite viewpoint as being untenable.

If you’ve got a few minutes and want to cause some bafflement among conservative pollsters, have fun with it.

Ken Ham commissions a scientific study

So right away, you know not to trust it. No details are given, we are simply told that “a major study he commissioned by a respected researcher unveils for the first time in a scientific fashion the startling reasons behind statistics that show two-thirds of young people in evangelical churches will leave when they move into their 20s”. That’s actually a nice result from my perspective…so it’s too bad that I can’t believe what he claims.

Also, since it is Ken Ham, he knows exactly what the problem is and what we need to do to keep more kids in the faith.

The book explores a number of reasons for the findings, but Ham sees one overarching problem that is related to how churches and parents have taught youth to understand the Genesis account of creation.

Ham — who believes in a literal six-day creation that happened 6,000 to 10,000 years ago — says the church opened a door for the exodus of youth, beginning in the 19th century, when it began teaching that “the age of the Earth is not an issue as long as you trust in Jesus and believe in the resurrection and the Gospel accounts.”

I get it. His “study” is actually propaganda for his “museum”.

Science wants to reward good online science education resources

If you’ve been building a site for science education, you’ll want to looking into this: The Science Prize for Online Resources in Education (SPORE).

The Science Prize for Online Resources in Education (SPORE) has been established to encourage innovation and excellence in education, as well as to encourage the use of high-quality on-line resources by students, teachers, and the public. In 2009, the prize will recognize outstanding projects from all regions of the world that bring freely available online resources to bear on science education.

Winning projects should reinforce one or more of the four strands of science learning recommended by the National Academies (Taking Science to School: Learning and Teaching Science in Grades K-8 [2007], National Academies Press; see also Bruce Alberts, “Redefining Science Education,” Science 23 January 2009: 323, 437) and be consistent with the science education standards published by the National Academies (National Science Education Standards [1996], National Academies Press) and the AAAS (Benchmarks for Science Literacy).

There are more details at the link. This is a non-trivial exercise, so don’t think you can put it together in a flash…but if you’ve got something you’ve been building for a while, look into getting some recognition for it.