…and this is a 
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.
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
Life Science
Comments
Posted by: Reginald Selkirk | June 17, 2009 3:06 PM
Off-topic Australian poll: Should marriage be limited to hetrosexual couples?
Posted by: Coturnix
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June 17, 2009 3:15 PM
Great review. Thank you.
Posted by: KeithB | June 17, 2009 3:18 PM
"I'd be designing rocketships right now"
Hey, a Biologist might come in handy designing a Vorlon Ship, or Tin Man:
http://en.wikipedia.org/wiki/Tin_Man_(TNG_episode)
Posted by: Tim Awake | June 17, 2009 3:24 PM
I love it when scientists cross disciplines and simply assume that because they know one field of study, they know the other. It leads to absolutely hilarious stuff, especially if you like to scavenge scientific papers/books for fiction ideas.
Posted by: littlejohn | June 17, 2009 3:27 PM
If you stare at the skull diagram long enough, you become one with the universe. I also realized I hate meerkats. Damn you, Discovery Channel!
Posted by: E.V. | June 17, 2009 3:27 PM
It sounds like ID woo: he just wrote the results to fit his beliefs.
Posted by: Fred the Hun
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June 17, 2009 3:33 PM
Meet this Material
Posted by: bam | June 17, 2009 3:33 PM
I remember a class in the history of my own field (anthropology) that taught me a lesson that I don't think was intended (given the professor's love affair with the anthropological version of structuralism). I realized that anything written by someone who sits in a chair and thinks is going to be very tough slogging indeed. If all you've got is ideas and not data you are not constrained to keep to the data and you can go flying off into nevernever land without even noticing--dragging moaning, helpless students after you. I'm not saying that "armchair" theorists are necessarily always wrong. In fact, they can come up with some amazing and useful ideas. But even when they do, reading about it is often like being disemboweled with a bamboo sword=slow and painful, even if it does get the job done eventually.
Posted by: Richard Harris
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June 17, 2009 3:35 PM
Fleury wants to claim that it is hydrodynamics, and fluid flow, and shearing forces.
That's trivially obvious. If the oceans had been molasses instead of water, natural selection would've selected a different set of genes.
Posted by: Glen Davidson
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June 17, 2009 3:36 PM
Physics is bound to affect life greatly, and yet organisms are hardly going to be optimized to fit with physical constraints.
He seems to think like a creationist projecting "god can do anything" onto their myth of evolution:
Or not. Since we have very good reason to think that evolution cannot innovate much beyond the basic tetrapod "body plan," coming up with an additional reason for such constraint tells us about as much as saying "design" does--nothing at all.
Are adult insects hexapods because eight legs won't do? Arachnids appear to do fine with eight, although it's true that they don't fly.
It's fairly easy to come up with a few examples of such evolutionary constraints which apparently don't involve physical constraints. That this nails the case, I don't know, but there's more evidence of evolutionary constraint on basic "body plans" than for physical constraints for same, thus far.
Glen D
http://tinyurl.com/6mb592
Posted by: eddie | June 17, 2009 3:37 PM
He seems to be implying, with the homo habilis skull, that there's some kind of streamline progression from early to later hominids, I mean more than implying anything about embryology of any particular hom.
Posted by: Enzyme | June 17, 2009 3:37 PM
The diagram at the end reminds me of a paper I sat through at a conference on Philosophy, Psychology and Psychiatry a couple of years ago. The speaker showed a slide of green and black stripes, and superimposed on it another slide of green and black stripes, offset at a slight angle.
Somehow - I forget how - this was supposed to demonstrate that (a) Descartes was right about the immateriality of the mind, which is (b) fractal; and (c) this tells us something morally important about murder's wrongness.
When the time came for questions at the end, there was just an embarrassed silence. We'd clearly just witnessed someone's nervous breakdown, and it seemed unfair to ask for clarification...
Posted by: Jerry Coyne | June 17, 2009 3:40 PM
Man, I'm glad YOU did this rather than I. We keep hearing that this kind of idea presages a revolution in evolutionary biology, in which natural selection will be relegated to a minor role. That revolution, however, always seems to be just a wee bit around the corner. . .
Posted by: Hoolicious | June 17, 2009 3:41 PM
As a biologist who studies the effects of physical and mechanical forces on cellular behavior, I am smacking my forehead in embarassment for this guy. There are so many interesting, testable, and legitimate points to make about how physical factors like fluid shear and isometric tension impact tissue morphogenesis! Like how cell shape changes lead to changes in gene expression, or motility, or even differentiation (via all your favorite cytoskeleton-associated signaling molecules). Oy vey!
I do apologize, PZ. I try to teach the physicists and engineers about biology, but I can't be everywhere at once.
Posted by: Wes | June 17, 2009 3:42 PM
So now, in addition to Pivar's Meat Doughnut Theory of development, we can add the Embryonic Swirly Theory.
How long before the DI starts demanding evo-devo "teach the controversy"?
Posted by: Sili
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June 17, 2009 3:52 PM
There's only one question that needs be asked: Who does Fleury know on the editorial board of The European Physical Journal: Applied Physics?
Posted by: Brock | June 17, 2009 3:52 PM
Ha. I was going to cut the guy some slack and shrug it off as an author being (despite perhaps an earnest attempt) out of his depth and lacking focus. But that swirly skull at the end is just plain stupid without mechanical measurements.
Although maybe if I stare at it long enough, I'll activate my hidden powers of echolocation :p
Posted by: miko | June 17, 2009 3:53 PM
yeah, there is a great (though not fully developed) literature on how cells and tissues sense, respond, and are constrained by mechanical forces. of course, they do it with gene products. this guy sounds like a well-intentioned crank.
Posted by: xebecs | June 17, 2009 3:54 PM
Paging the attorneys representing whoever now owns The Twilight Zone.
Posted by: Sili
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June 17, 2009 3:59 PM
Speaking of nutcases: Whatever happened to that guy who seemed to descent into schizophrenia halfway through a conference paper? I think he poster very angrily in the comments on the post, but I don't recall hearing anything about him getting help.
Posted by: Flex | June 17, 2009 4:08 PM
What?!?
That's not an x-ray of the bionic man while he's using his super-hearing and super-vision? Na na na na na naaaa.
No. Wait.
It was the bionic woman who had the super hearing.
My mistake.
Posted by: oldcola | June 17, 2009 4:10 PM
PZ thank you and I have a hard time to tell you my joy to have an expert's opinion.
Some beer should be involved in that.
I'm reading/correcting and blogging step by step. As you say he read a lot. But he report in a quite weird way, sometimes without any connection with the cited paper and that's as much weird. I wouldn't expected you to check every single assertion and pinpoint errors, I'll will handle that the best I can do.
Help from pharyngulites is welcome. The paper is Open Access and my comments posted here.
I'm preparing the list of errata to send to the The European Physical Journal: Applied Physics Editor in Chief.
Thanx once more (I'll double vote to any poll you post)
Posted by: pedant | June 17, 2009 4:13 PM
"It's rather tautological, for one thing, but it is also trivially true"
-> I might be too accustomed to speaking loglish, but i'm fairly sure this sentence is itself a tautology.
Great read, though- i'm reminded of Dennett's warnings against 'greedy reductionism'.
Posted by: Wes | June 17, 2009 4:21 PM
I don't think it's a tautology--because it could come out false if the sentence it is describing is not itself a tautology. Remember that a tautology would come out true in all possible worlds.
It may be a redundant conjunction (depending on what one means by "trivially true"), but "(A & A)" is not a tautology.
/pedantry
Posted by: Wes | June 17, 2009 4:24 PM
I don't think it's a tautology--because it could come out false if the sentence it is describing is not itself a tautology. Remember that a tautology would come out true in all possible worlds.
It may be a redundant conjunction (depending on what one means by "trivially true"), but "(A & A)" is not a tautology.
/meta-pedantry
Posted by: pedant | June 17, 2009 4:38 PM
All I meant was that 'trivially true' and 'tautology' mean the same thing, making the sentence read like "not only is it rather tautological, for one thing, but it's also rather tautological". I totally could be wrong about 'tautology' and 'trivially true' meaning the same thing, of course.
Posted by: 'Tis Himself, OM
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June 17, 2009 4:38 PM
That's what happens when a biologist ventures into economics, he gets just part of a definition.
Specie is any type of hard money or commodity money (as opposed to fiat money). The gold in Fort Knox isn't coined but is specie.
Commodity money is money whose value comes from a commodity out of which it is made. It is objects that have value in themselves as well as for use as money.
Examples of commodities that have been used as mediums of exchange include gold, silver, copper, salt, peppercorns, large stones, decorated belts, shells, alcohol, cigarettes, cannabis, candy, and grain. These items were sometimes used in a metric of perceived value in conjunction to one another, in various commodity valuation or price system economies.
Posted by: F | June 17, 2009 4:38 PM
Are we sure he didn't base this entire paper on the logo artwork from some artist or band? The swirlyskull just screams "pop adolescent rock artwork".
Posted by: cervantes
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June 17, 2009 4:39 PM
Hmm, however ridiculous this paper, it does pique my curiosity about something. Some tetrapods have lost limbs -- snakes, whales -- but none have gained any. Sometimes extra limbs arise in embryos from what I presume are teratogenic effects, but is there any reason why genetic mutation couldn't give an embryo one or more extra limbs? And might not such a feature turn out to be useful? It's interesting that evolution has never produced a 5- or 6-limbed tetrapod (which would be a misnomer, I suppose, but mutation and natural selection don't know anything about the name). In order to gain the use of our arms, we had to give up the use of our front legs as legs -- but there are no centaurs. Curious that.
Posted by: AdamK | June 17, 2009 4:51 PM
And no four-legged, winged dragons, dammitalltohell.
Posted by: MJ | June 17, 2009 4:51 PM
"...assume a spherical cow."
Posted by: Equisetum | June 17, 2009 4:55 PM
"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."
That's exactly the feeling I got reading 'How the Leopard Changed it's Spots' by Brian Goodwin. It seemed like he was trying to rewrite development to make genes unnecessary, and I kind of dismissed his ideas. Of course there's physics involved, just as in everything, but it's the genes that are guiding the physics, I think.
Is there more of Goodwin's work out there that's accessible to the layman?
Posted by: rob | June 17, 2009 5:25 PM
"Please show me cell movements or tensions in the developing skull that correspond in any way to those psychedelic lines. It's completely nonsensical."
it's not completely nonsensical. the field lines look like the magnetic field lines due to a current loop, as viewed from the plane of the loop. so obviously that skull has some sort of circular ion flow between the eye orbits and ear orifices that, um, makes a magnetic field, that um, causes um.
well, okay, it is nonsensical afterall.
Posted by: chaos_engineer | June 17, 2009 5:28 PM
But is there any reason why genetic mutation couldn't give an embryo one or more extra limbs?
I think the problem is that a "fully developed" leg is so complicated that it's impossible to get a mutation that would add functional new legs. (You could get a developmental mutation that duplicated existing legs, but the new legs wouldn't have the fine-tuning to work well in their new position.)
So the number of limbs can only be set in the early stages of their evolution...think segmented worms that are starting to develop leg-like protrusions. Adding or subtracting a segment is no big deal, but later on the individual segments become more specialized, and it gets harder to change their structure.
Posted by: Tim H | June 17, 2009 5:48 PM
The problem would be in developing the support structure for the limbs, wouldn't it? You would need a second set of hips between the shoulders and pelvis. It would have to differ from both, being a "middle" set rather than an "end" set. It would take one monsterously improbable mutation just before the pharyngula stage (see, I leaned something from P.Z. when he came to Champaign) to pull that off.If a third, middle, pair of limbs DID evolve, however, it would probably be much easier, by simple duplication, to evelve a fourth and fifth set. Right?
Posted by: josh | June 17, 2009 5:48 PM
Speaking for physicists worldwide, please don't blame us for this guy's interdisciplinary peregrinations. I mean, it is all physics when you get down to it (plus logic) but that's in the sense that the structure and operation of genes along with everything else is physics. That doesn't mean that a) a biologist can't say highly intelligent things about development without fully reducing it to precise molecular forces, or b) a physicist can apply macro level analyses like fluid dynamics to a highly complex system which we have every reason to think depends crucially on "micro" level variables, i.e. genes.
I'd be very interested to know what constraints fluid dynamics,etc. put on developing organisms, but that skull diagram is like a flashing sign: "Actual Equations Applied To Actual Data Not To Follow". It seems obvious to this non-biologist that you can't ignore the effects of genes and genetic pathways on form in light of the confirmed success of genetics.
He seems to posit that genetics can be translated into a few relevant flow parameters (viscosity?) and then, given an initial asymmetry,the final form is determined. Looking at the enormous diversity of form across species and the relatively well conserved forms within a species I can't imagine this approach being fruitful.
Posted by: KeithB | June 17, 2009 6:05 PM
"But is there any reason why genetic mutation couldn't give an embryo one or more extra limbs? "
It happens. Didn't that Indian girl get an extra set of arms?
However, getting the new limbs hooked up to the skeleton in a practical way may be tough, too. Extra limbs are interesting, but if they aren't hooked into some kind of hips or shoulders they aren't much use.
Sometimes it is better having an exoskeleton.
Posted by: KeithB | June 17, 2009 6:09 PM
Oh, and I don't think "Clarifying" means what Fleury thinks it means. I think "Inconceiveable" works better in the context of his paper. 8^)
Posted by: frog | June 17, 2009 6:57 PM
The unfortunate problem is that physicists don't do biology -- it's too hard -- and biologists don't do physics -- most can barely add.
But it seems obvious that those "developmental" genes must be expressed via physical interactions. They're not programs in a computer -- they are constraints on a physical transformation. Unfortunately, that metaphor sticks in people's minds...
Now, the fact that biologists have found molecular biology and genomics easier doesn't say much to me about it's relative value: what gives you a quick bang for the buck may definitely be a cul-de-sac.
How do cells decide about their migratory paths or when to apoptose? Those must be driven primarily by physical cues, not abstract "signals" like pointers in a computer program. Squish me, and I do one thing; poke me and I do another -- those aren't are pure signals, but a convolution of signals (arbitrary phenomena) and really getting poked and squished.
Unfortunately, doing that well would require a lot of very hard mathematics. And those who know such fields like topology (what I would love to see a good application to embryology!), often know too little about the application to avoid sounding like or becoming crackpots.
Posted by: Nichole | June 17, 2009 6:58 PM
@ #37: Yeah, and that British dude with the twelve, fully functional fingers? I mean, maybe there just... was room for them...?
So, uh, science enthusiast but layman here..
This paper reminds me greatly of Sagan, when he extemporizes on the lifeforms of Jupiter's upper atmosphere in "Demon Haunted World." He just sounds... implausible. I can't explain why. A biologist would doubtfully do a better job. But it has that "overmyheadedness" feel to it. An astronomer should stick to what he's good at. As should a physicist. Until we have that "unifying theory of everything." Because people call biology a "soft science" but I think that just means they don't get it.
Posted by: Alan Kellogg | June 17, 2009 7:11 PM
Let me see if I got this correct; a limb grows from one of four patches of tissue. The whole process in complex, including the development of a number of supplementary structures that work together to produce the integrated structure we call a limb. On occasion an extra patch appears, but the suite of gene interactions necessary for a complete limb is not available, so a complete limb does not arise.
In the case of dragons and griffins and similar hexapedal tetrapods the embryo develops six such patches, though it is possible the forelimbs and wings arise from a patch that incorporates a more complex sequence of developmental events. Obviously this only applies in worlds with dragons and griffins and similar hexapedal tetrapods.
Yes, ladies and gents, it is possible for science to shape fantasy; if you're able to see things differently. :)
Posted by: Blake | June 17, 2009 7:29 PM
ehhhh, I think the difference Nichole, is that Sagan would have FALLEN ALL OVER HIMSELF to immediately make perfectly clear that he was speculating wildly, and for fun (Mr. X?.... is that you?), when asked about his Jupiter blob squid things. Where as Dr. Kookinstein here seems totally serious about his "theories".
Posted by: JimF | June 17, 2009 7:31 PM
Did he call that a Homo habilis skull? It's not; that's a drawing based on the Peking Man (Homo erectus) skulls.
Posted by: Tommy Traddles | June 17, 2009 7:36 PM
PZ,
Now I understand why you don't post much science stuff.
Judging by the number and content of the replies here, apparently not many people give a shit about science.
Bashing creationists is much more fun.
Posted by: David Marjanović, OM | June 17, 2009 7:56 PM
<headdesk>
I was taught where the lateral-plate mesoderm comes from in the last years of highschool. I have a hard time imagining that that's not done in France, Belgium, or Switzerland.
Nope. She gastrulated twice, and only one side had enough room left to form a head. In the end, the two bodies (each complete with two legs and two arms) were cut apart...
Development follows Murphy's Law. Vertebrate development follows O'Toole's Commentary on Murphy's Law.
Posted by: vincent Fleury | June 17, 2009 8:09 PM
To whom it may concern
may be weird, ok.
Let me take it as a compliment, especially as compared to the rest of the opinions on anything that scratches in any minute way your prejudices.
A very moderate and in some form interested review; the paper does not fare too bad after all, considering the gap between concepts.
Time will tell, and it takes time to turn one's head.
Thanks for reading it anyway, it's only a small seed.
You can get more info about my work, including a few animations at
http://www.msc.univ-paris-diderot.fr/~vincent.
Most of the comments here above are irrelevant, for example up there : Lakshmi, the little indian girl with many limbs was a case of fetu in fetu (a cojoined twin absorbed inside the body), nothing to do with extra limbs.
I would be happy to send force measurements in the limb areas to any fellow scientist.
I apologize for the english mistakes, I would certainly have written a better paper in french. Please forgive all the english mistakes you might find on my website.
Best regards and please continue with this interesting blog.
Vincent Fleury
Posted by: vincent Fleury | June 17, 2009 8:14 PM
To whom it may concern
may be weird, ok.
Let me take it as a compliment, especially as compared to the rest of the opinions on anything that scratches in any minute way your prejudices.
A very moderate and in some form interested review; the paper does not fare too bad after all, considering the gap between concepts.
Time will tell, and it takes time to turn one's head.
Thanks for reading it anyway, it's only a small seed.
You can get more info about my work, including a few animations at
http://www.msc.univ-paris-diderot.fr/~vincent.
Most of the comments here above are irrelevant, for example up there : Lakshmi, the little indian girl with many limbs was a case of fetu in fetu (a cojoined twin absorbed inside the body), nothing to do with extra limbs.
The black lines superimposed on the skull are the dipolar component of the deformation field. A very simple concept. You may find animations of skull evolution at following this scheme at:
http://www.msc.univ-paris-diderot.fr/~vincent/englishanimationsoeuf.html
I would be happy to send force measurements in the limb areas to any fellow scientist.
I apologize for the english mistakes, I would certainly have written a better paper in french. Please forgive all the english mistakes you might find on my website.
Best regards and please continue with this interesting blog,
Vincent Fleury
Posted by: vincent Fleury | June 17, 2009 8:17 PM
To whom it may concern
may be weird, ok.
Let me take it as a compliment, especially as compared to the rest of the opinions on anything that scratches in any minute way your prejudices.
A very moderate and in some form interested review; the paper does not fare too bad after all, considering the gap between concepts.
Time will tell, and it takes time to turn one's head.
Thanks for reading it anyway, it's only a small seed.
You can get more info about my work, including a few animations at
http://www.msc.univ-paris-diderot.fr/~vincent.
Most of the comments here above are irrelevant, for example up there : Lakshmi, the little indian girl with many limbs was a case of fetu in fetu (a cojoined twin absorbed inside the body), nothing to do with extra limbs.
The black lines superimposed on the skull are the dipolar component of the deformation field. A very simple concept. You may find animations of skull evolution following this scheme at:
http://www.msc.univ-paris-diderot.fr/~vincent/englishanimationsoeuf.html
I would be happy to send force measurements in the limb areas to any fellow scientist.
I apologize for the english mistakes, I would certainly have written a better paper in french. Please forgive all the english mistakes you might find on my website.
Best regards and please continue with this interesting blog,
Vincent Fleury
Posted by: David Marjanović, OM | June 17, 2009 8:57 PM
Donc il est vrai, Monsieur ? Vous n'avez pas appris à l'école (en Te, j'imagine) d'où vient le mésoderme des plaques latérales ? Et vous n'avez même pas essayé de parler à des gens qui font de l'évo-dévo -- il y en a à Paris 6, donc probablement sur le même campus que le vôtre ?
(En outre, le message d'erreur indique "ne resoumettez pas votre commentaire". Le commentaire a bien passé, ce n'est que la page qui refuse de se recharger correctement après. Donc vous avez déjà répété votre commentaire deux fois.)
Posted by: a_ray_in_dilbert_space
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June 17, 2009 9:02 PM
Vincent, Bienvenue!
It appears to me that your work on limbs could have been motivated somewhat by the study you published in Phys. Rev. E on vascularization. The Phys. Rev. E work appears a bit more plausible to me than this. However, I too am a physicist, and my field of expertise is very far removed.
I also suspect that your lengthy survey of biology might have been due to your intended audience being mainly physicists. Correct?
For those interested, here's a press release on the Phys Rev E paper.
Posted by: a_ray_in_dilbert_space
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June 17, 2009 9:08 PM
Oops, the link didn't come through:
http://www2.cnrs.fr/en/1204.htm
Posted by: gorobei | June 17, 2009 9:11 PM
Try "Invention and Evolution" by Michael French. No just-so-story stuff about how it got there, just serious engineering analysis of the form observed. He hits all the good stuff (power/weight analysis of flight, regenerative systems, etc.) I find myself rereading this book every few years.
Posted by: efrique | June 17, 2009 9:13 PM
Wow I bet there's a bunch of physicists who submitted legitimate-but-rejected-for-reasons-that-boil-down-to-lack-of-space papers to that journal who are absolutely livid right now.
I've noticed this attitude among a subset of physicists - that phsyics somehow underlies everything (which in a trivial sense it does, of course), so they (the subset) think they can go in and revolutionize some field or other with a few months work siiting in a chair. There have been physicists that have moved into other areas and done great work - I can think of several. They usually had to spend years at it first, though, and actually do experiments once they get there. The ones who think they can do it on the quick usually miss a few basic but vital bits of information, which kind of screws up the whole bit of theorizing, and wastes the opportunity (and everyone's time). A pity really - no doubt a proper collaboration could produce some nifty insights now and again.
Posted by: airbagmoments | June 17, 2009 9:45 PM
Would you consider Stephen Wolfram's work in the biological portions of "A New Kind of Science" to be structuralist or something...else?
Posted by: Troy Britain | June 17, 2009 10:30 PM
Foley beat me to it, it's definitely a reconstruction of Peking Man, not H. habilis.
Posted by: Charlie Foxtrot | June 17, 2009 10:51 PM
Gah! All hail Hypno-Skull!
Posted by: PZ Myers
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June 17, 2009 10:52 PM
Every word of the caption under the skull is taken directly from the paper.
Posted by: Merrydol | June 17, 2009 11:27 PM
Tommy @ 44,
I think a lot of folks probably just lurk around the science posts. There's not as much opportunity for debate for the non-scientist readers (and those of us in totally different fields), but they're still fun posts to read!
Posted by: meh1963 | June 18, 2009 12:37 AM
Hah...#54 got there first. I am also wondering if Stephen Wolfram's work falls into the categories you set forth.
If I'm reading this correctly (math/physics perspective, not biology), structuralists confuse algorithmic complexity with the mechanics of gene expression....
Posted by: ninjaneer | June 18, 2009 1:00 AM
KeithB, a biologist would also come in handy for designing an astrochicken:
http://en.wikipedia.org/wiki/Astrochicken
Posted by: oldcola | June 18, 2009 2:52 AM
Vincent Fleury, as you seem to be in a cooperative mood, could you address please the problem raised here:
citing one of his papers where a single measure of Fgf10 expression is shown and no pressure measures. Absence of pressure measurements being acknowledged in a public conference.How can one assert:
Posted by: madhu | June 18, 2009 3:04 AM
Entertaining review! And that part about students trying to review entire fields resonates after recent grading of term papers.
Speaking of structuralists (and I'm a fan of good old D'Arcy), esp. ones perhaps taking it too far, I have to ask what (if anything) you think of J Scott Turner's "A Tinkerer's Apprentice"? Have you reviewed it? A colleague handed me a copy a while ago, but I haven't managed to make it past the first couple of chapters. Any thoughts?
Posted by: vincent fleury | June 18, 2009 3:30 AM
@50Thanks for the welcome
but it is unlikely I will debate on this forum.
Although there are a number of comments I would anywhere else feel happy to respond to, they are smothered by quite a few hopeless comments or brutal attacks which have some sort of a bad breadth.
To answer your comment, yes, It was a physics paper, intended for physicists in a physics journal, so it makes little sense that somebody like Prof. Myers tries to review it, and then complain about the lengthy and tedious introduction. I find it weird that Prof. Myers should not be able to understand that a text is always intendend for a certain audience, it was not for people like him. I notice he goes down to very low semantic comments, over triffles, but is unable to understand the physics of deformation rate fields (Stokes creeping flow), too bad. I can't blame him for that. I find it somehow sad that he should put forward some mean comments about english mispells. We foreigners have already a big pain to write in english. Maybe he could balance a few mispellings with the effort of writing all the rest in english. I wonder how many pages he could himself write in any foreign language. Anyway, it is very odd how he tries to infer things from mispellings "procès d'intention", we say in french. All foreigners who submit articles to english-speaking journals may recognize one dark side of the english tyranny.
Anyway, returning to science, I find it also odd that I should be charged with being some sort of a theoretician physicist throwing out ideas out of the blue from an armchair. I am an experimentalist working all day with embryos. I see that a confortable way of dismissing any interesting work is just saying that the author is a theoretician-physicist, how sad.
This being said, I find it also very odd that Prof. Myers should not have spotted in the paper all the experimental data. Probably the readers of the article, if any, will reset the truth for themselves, a few comments by Prof. Myers are clearly deffamatory; not quite convenient.
About the lateral plate thing, oh boy, all too ridiculous. If he has read the paper honnestly, he should have noticed that it was referring to the lateral plates in the limb field. There are indeed four bumps in the presumptive hips and shoulder areas of embryos (see a 3rd day of development in a chicken) and nowhere in biological articles you find an explanation for these bumps, or gentle curvature of the lateral plates, or whatever you feel like calling it. That really is the issue, you need a physics force to generate these bumps, by fundamental laws of nature (this is what physics means, by the way). Waving hands about words is really low.
To finish, let me say that the very fact that Prof. Myers has read and reviewed this paper is interesting. It is the symptom of something good: that he, and others, do not actually know how the tetrapod plan, and eventually human body is established. Otherwise, he would just have written something like
"it is well known that limbs are formed by.... so that the origin of tetrapods, including humans is..." and it would be the end of it, my paper would not even deserve a single word.
The truth is that limb positioning and development is ascribed to genetic inductions, which is not the case. The origin of tetrapod bauplan is a hyperbolic flow originating in the fact that development has to pass through a 4-cells stage. The paper explains it all, with proper references to all the accumaulating data on flows in early formless blastulas. Think of a round blastula, it is transformed into an embryo by a hyperbolic flow.
Best regards, to you too, M. Myers, you are a decent person, probably a good man and father, and and may be you even voted Obama. But nobody is perfect : you are not very open minded.
Vincent Fleury
Posted by: Beelzebub | June 18, 2009 3:55 AM
@62 "A Tinkerer's Apprentice" is brilliant, much more cogent than anything in the paper PZ just reviewed.
Posted by: oldcola | June 18, 2009 4:35 AM
@#43 Thanks for the Oops!
@#63 Dr Fleury, I did asked a question about your experimental work and your conclusions from it.
Posted by: vincent fleury | June 18, 2009 4:45 AM
@every skeptic
the psychedelic thing is the writing of the deformation rate field, works on all skulls. Apparently, biologists are not used to these charts (Stream functions iso-curves). In terms of "origin of man" concept, it relates the origin of forms to the dynamics of deformation rate fields (viscous materials),acting on a sphere. It is the "origin of man", in the same sense that the wind over the sea is "the origin of waves".
It is better understood by actually viewing the "film" of the deformation of the head under the said deformation rate field. It is found at this address :
http://www.msc.univ-paris-diderot.fr/~vincent/animationsoeuf.html
there was a still picture in the paper which Prof. Myers skipped, or may be he did not understand the link between equations and morphogenesis (moving boundary problem).
I am sorry for publicizing this to this audience, and I do not want to intrude across your debates. But please consider this as a "right of reply" or whatever you call it in english.
And let me say good bye.
Vincent Fleury
Posted by: Bernard Bumner
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June 18, 2009 6:18 AM
So, Vincent Fleury turns up to defend his conclusions, without actually addressing the real meat of the complaint; that the basic premise upon which those conclusions are predicated may well be flawed due his neglect of the established molecular and genetic basis for ontogeny.
At the very least, he is guilty of offering for publication (as the journal, editor, and referees are also guilty of accepting) a paper which is poorly assembled and would have benefited massively from the input of a good developmental biologist. If he has good data, in need of explanation, then he has succeeded in burying it well.
At worst, he is positing novel explanations for phenomena already better explained by the conventional interpretation of other data.
I think that science (along with Vincent Fleury himself) has not been well served by the editorial board of this journal. Sadly, this king of thing seems to be increasing common, what with more and more journals becoming ever more desparate for original research articles.
Posted by: Bernard Bumner
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June 18, 2009 6:21 AM
I may have misplaced a royal in that last post...
Posted by: Confuseddave
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June 18, 2009 6:44 AM
...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.
Not actually true - certainly not in the chicken (can't exactly speak for other organisms, sadly - but the mesoderm (a bunch of it, at least, lateral plate included) is formed by the primitive streak and it's come from a few fate mapping studies that it's the position along the streak that defines what type of mesoderm it'll become - so cells at the top go into the midline (with the node giving rise to the notochord among other things), cells in the middle become paraxial mesoderm, and cells further down become lateral plate. Fish and frogs might be weird, but I'm fairly sure that's how amniotes make their lateral plate.
Still, the point remains that while there may be controversy about *how* it's made, it's not quite that we don't have a clue.
Vincent: Hi! I've come across your claims before (I work in the same department as Kees Weijer, whose work on gastrulation I understand you've butchered somewhat over the years).
it makes little sense that somebody like Prof. Myers tries to review it, and then complain about the lengthy and tedious introduction.
You miss the point. Many reviews have long and tedious introductions. His point was that your introduction did not support your hypothesis. I don't care what field you're writing for, in scientific literature you have to pare down to the minimum that illuminates your problem.
I find it somehow sad that he should put forward some mean comments about english mispells. We foreigners have already a big pain to write in english.
Then get a competent native speaker to proofread it. It's not complicated; I freqently proofread papers written by non-native speakers in my lab.
About the lateral plate thing, oh boy, all too ridiculous. If he has read the paper honnestly, he should have noticed that it was referring to the lateral plates in the limb field. There are indeed four bumps in the presumptive hips and shoulder areas of embryos... and nowhere in biological articles you find an explanation for these bumps, or gentle curvature of the lateral plates, or whatever you feel like calling it.
That's even worse! The origins of the lateral plate are at least a little vague, the origins of the limb buds are really well known. You've apparently missed the really famous classical experiments (in amphibians, if I remember, but a similar thing is done in chickens) where grafts of the overlying ectoderm into different regions causes new bumps (we call them limb buds) to form from naive lateral plate. It really is very well established that signalling molecules from the embryonic "skin" cause the limb buds to form by differential proliferation of the cells, not some intrinsic physical field - in fact, it's so well established that you can stick a bead soaked with said signalling molecules into the flank of a developing embryo and induce an extra limb.
If you want to convince me that your daydreaming is a genuine challenge to this model - after all, it is only a model, and there are always alternative explanations - you're going to need a pretty big pile of experimental data to back it up.
You really are an embaressment to all physicists working in biology. And unlike PZ, I know a few who do make damn good biologists (Julian Lewis is the one who springs to mind).
Posted by: Confuseddave
|
June 18, 2009 6:48 AM
Dammit, I messed up the formatting in my last post and it's impossible to read. Gah!
Posted by: Gerdien | June 18, 2009 7:23 AM
Don't fish have pectoral, pelvic and anal fins?
If so, are three pairs of fins early or late in fis-descent terms? And if the tetrapod ancestors too had pectoral, pelvic and anal fins, why are we not hexapods? and, do hind limbs correspond to pelvic or to anal fins?
Or do I not know enough about fishes?
Posted by: Gerdien | June 18, 2009 7:23 AM
Don't fish have pectoral, pelvic and anal fins?
If so, are three pairs of fins early or late in fis-descent terms? And if the tetrapod ancestors too had pectoral, pelvic and anal fins, why are we not hexapods? and, do hind limbs correspond to pelvic or to anal fins?
Or do I not know enough about fishes?
Posted by: Confuseddave
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June 18, 2009 7:26 AM
I tell a lie - the signalling does in fact come from within the lateral plate mesoderm. I was confused because later on FGFs are produced by the AER in the ectoderm as the limb bud extends.
Limb development begins when mesenchyme cells proliferate from the somatic layer of the limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) These cells accumulate under the epidermal tissue to create a circular bulge called a limb bud. Recent studies on the earliest stages of limb formation have shown that the signal for limb bud formation comes from the lateral plate mesoderm cells that will become the prospective limb mesenchyme. These cells secrete the paracrine factor FGF10. FGF10 is capable of initiating the limb-forming interactions between the ectoderm and the mesoderm. If beads containing FGF10 are placed ectopically beneath the flank ectoderm, extra limbs emerge (Ohuchi et al. 1997; Sekine et al. 1999).
From Gilbert, an undergraduate textbook on Developmental Biology, freely available at NCBI's pubmed.
See, this is a model supported by a thing called evidence. It may turn out to not be true, but to show that, you're going to need more evidence of your own that explains all of these observations and more. Self-indulgent postulating about unsupported cell movements is not going to cut it.
Posted by: Anonymous | June 18, 2009 7:33 AM
What your commentary reminds me of is the embryology work done by another famous mathematician: Alan Turing. I just finished reading an excellent biography of him (The Enigma), and here's what he did to try and explain chirality/asymmetry in embryonic development:
1. Picked chemicals that were involved in development.
2. Figured out which reactions would cause differentiation of form.
3. Simplify 1 and 2 until the computer he was running at the time could model it.
The result was an organism consisting of nothing but a ring of cells (a "simplification" of a worm), which formed an inside and an outside through chemistry.
I'm not a biologist, and perhaps that makes all the difference. But Mr. Turing did little speaking with embryologists at the time, mostly chemists. The only difference between him and this guy -- which is a lot -- is that his assumptions and limitations were clearly stated up front. Despite this, he got published through some friends whom he impressed -- most likely, by the computer work, not the biology.
Have you read his paper? Would you similarly criticize his research?
Posted by: Confuseddave
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June 18, 2009 8:16 AM
Also, scanning the paper, I came to this gem on segmentation:
In addition, when the embryo is split, the somitomeres form everywhere at the same time, and not in a sequential fashion following [Hensen's node], thus suggesting a direct effect of shear along the fold (some sort of buckling).
I'm going to be generous and allow that you're too incompetent to understand the subtleties of this 1983 experiment versus EVERYTHING ELSE IN THE SEGMENTATION FIELD, and not an inveterate liar who is deliberately cherrypicking his data.
With this in mind, I can direct you to a large number of papers using experiments in which the embryo is split in two, and the result is sequential formation of somites. It's the basic experiment of any somitogenesis lab.
Start with Isabel Palmeirim's paper on Hairy1 - look at figure 5. Try Yasumasa Bessho's 2001 paper to see the same thing in the mouse (figure 1 E-G). Of course, these are only short cultures - so try Sarah Gibb's paper from 2009 - some of those half embryos were cultured for nearly four hours (check out figure 2). Guess what? Regularily formed segments, one every 90 minutes. Heck, I've done this technique myself.
Your ignorance of the field you're intent on revolutionising is laughable.
Posted by: Confuseddave
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June 18, 2009 8:23 AM
Gerdian - that's a really interesting question. My cursory scan tells me that the anal fins are unpaired, like the dorsal fins and tail fins, and have a separate developmental origin.
YMMV, IANAD (in fis development, anyway).
Posted by: Gobaskof | June 18, 2009 9:00 AM
The psychedelic drawing seems to be attempting to show equipotential lines (analogous to a electric field, thus assuming an incompressible fluid). There seem to be sources or sinks for the fluid at the eye socket and ear hole (Ear hole is scientific yeah?). So this would assume that all flow travels through lines perpendicular to these equipotential lines.
What the diagram deems to be getting at is that the flow line is the skull. If we examine the flow along the top of the skull we get fairly good agreement. But where the head goes pointy at the back, or around the jaw the skull is far from perpendicular to the equipotential lines.
Similar psychedelic lines are often used for simple fluid dynamics (Maybe for more complicated problems as well, I am only an undergrad, what do I know?), but the relevance stops there, the lines and the skull don't match up.
Apologies for the long post.
Posted by: vincent fleury | June 18, 2009 9:24 AM
you got it almost right : these are not isopressure lines, but stream lines, it is not V=-grad(P), with V perpendicular to pressure levels; it is V=curl(Psi), with V parallel to stream-function levels, at last a little candlelight in this biologists' darkness. Anyway, you are better than the previous fellows, congrats.
Posted by: AJS | June 18, 2009 9:58 AM
If you want to talk about toilet drain behaviour, consider this. American toilets are generally of the syphonic pattern. There is a bowl with a drain hole at the bottom, and a waste pipe bent into an "S" shape, exiting vertically downwards through the floor. A constriction in the waste pipe slows down the exit of the bowl contents, allowing the flushwater to rise temporarily above the level of the trap weir, and creating a partial vacuum when it eventually enters the wide section after the constriction. The bowl contents are then drawn out by this partial vacuum (or forced out by atmospheric pressure). This constriction, and the awkward path of the waste pipe down, across, up, over and down, mean that this pattern of toilet is ever-plagued by the possibility of blockage.
British, European and Australian toilets are generally of the Washdown pattern -- basically a simple U-bend at the bottom, with a large bell-mouth. The exit from the basin is horizontal and without any constriction. There is no partial vacuum formed during flushing; instead, the basin contents are forced out by the descending flushwater. This design is practically immune to blockage as the pipe is full-bore all the way (110mm. is the UK standard).
My new one installed last year uses 6 litres of water for a full flush, which is meant to be enough for "big business" including paper; although a part flush (3l.) usually does the job.
Posted by: Stephen | June 18, 2009 10:49 AM
As a physicist, I have to say -
Are we sure this guy isn't an engineer?
Posted by: Bernard Bumner
|
June 18, 2009 10:50 AM
Unfortunately, Vincent seems seem determined to continue to defend his "hydrodynamic explanation", and seems to be not at all concerned with the apparent deficiencies of his model (or, at least, his presentation of it in this paper) with respect to observed molecular biology and genetics.
The best form of defence is not always attack, and if his colleagues were embarassed, then it does not make them right.
There are numerous and egregious errors, pointed out here and elsewhere - it is far from just PZ who has noted problems. It seems rather churlish to characterise one critic as incompetent whilst failing to address the substance of their critique, and simultaneously ignoring a large number of others who share similar concerns.
I wonder whether he is at all willing to admit that some of the biology-related content of the paper is incorrect? It is very sad that a physicist, publishing in the field of biology, feels the need to pretend that this is simply a matter of biologists failing to understand physics.
Posted by: emote_control | June 18, 2009 11:38 AM
"at last a little candlelight in this biologists' darkness."
Sounds like something a creationist or antivaxxer would say. We scientists who actually study the organisms in question are deluded into thinking we possess understanding, when we are actually scrabbling along by our fingers in the darkness. Only by accepting the half-baked blatherings of the enlightened outsider who descends from the Olympus of [whatever it is they're interested in] can we begin to truly SEE.
I'm sorry, Fleury. We've heard that line before. You're going to have to do better than passive-aggressive hostility to convince anyone that your ideas aren't just a Time Cube.
Posted by: WRMartin | June 18, 2009 12:58 PM
I call BULLSHIT. Those are vortices from the Windmill Car. Time Cube my ass.Posted by: David Marjanović, OM | June 18, 2009 1:41 PM
Well, no. You need Shh (sonic hedgehog) to generate an outgrowth from the body wall, and then a similar signal protein to induce the lateral-plate mesoderm to follow that growth. That's all.
Then why did the pectoral fins appear before the pelvic ones (and before the origin of jaws, incidentally)? The Osteostraci, which are closely related to the jawed vertebrates, have well developed pectoral but no trace of pelvic fins. (L'auteur de ces pages, Philippe Janvier, est ici au Muséum, vous pouver parler avec lui directement.)
Posted by: David Marjanović, OM | June 18, 2009 1:44 PM
Oh fuck.
I've started making the kind of mistake that only native speakers make.
AAAAAAARGH!!!
Out of here, out of here, out of here!!!
(FYI: correct would be vous pouvez, which is pronounced the same way.)
Posted by: Blake Stacey | June 18, 2009 2:06 PM
Let me Google that for you.
Turing did his work in a time when scientists knew much, much less about the genetic regulation of development than we know today. He could not know the future, but those physicists and computer scientists who attempt to pull a Turing today should know the present.
Posted by: Steamshovelmama | June 18, 2009 2:31 PM
Well, that's all very... bizarre...
Layperson, here. Self-educated in biology enough to follow PZ with ease, physics almost non-existant so other than to say I don't actually get what argument Dr Fleury is making - apparently removing the directional influence of genes from the theory of development seems... extreme. And by definition the processes of embryo development are subject to, carried out by and confined by the laws of physics and chemistry. To say so is a trivial statement.
However what really surprises me is Dr Fleury's response which does nothing to defend or correct PZ's interpretation of his article. His tone is patronising and offensive - and I'm fairly sure this isn't down to the second-language thing. In fact he comes across like any other mindless internet troll. If it I hadn't been reading this blog and had the response introduced by PZ that's exactly what I would have thought he was.
I'm not expecting meekness or humility - PZ was forthright in his views and I'd expect Dr Fleury to be just as outspoken but the level of vindictiveness and ad hominem attacks in his reply is quite worrying in a (presumably) reputable scientist.
Posted by: Timothy (TRiG) | June 18, 2009 4:41 PM
Can I just say thanks to AJS (#79) for a very informative post. I'd wondered what caused the odd sucking behaviour of American toilets.
TRiG.
Posted by: Rod | June 18, 2009 5:50 PM
OK, now don't yell at me because I didn't try to find an answer myself...I have to start dinner soon. I'm fairly familiar with evo-devo stuff...Hox genes, signaling gradients, etc. The basics. I don't have an intuitive problem with trying to reduce some of the initial processes to physics and equations, but only for things that are symmetrical. How would that begin to explain things that are asymmetrical? Like, why does the appendix end up on the right side in most people, whether they are right or left handed? I understand that the primary cilium may determine the "handedness" of an organism, but right and left handed people are not true mirror images. How would this type of thing ever be described by equations...of flow, pressure, etc?
Posted by: Kemist | June 18, 2009 5:54 PM
I think this guy's french, isn't he ? He makes other mistakes which suggest so ("apparance"; french is my first language, and this guy writes like somebody who doesn't really care about proper english synthax - he writes frenglish).
I think the mistake comes more from that fact than from him being a physicist. This in itself shows sloppiness in the review process, both on his end and on the journal's.
But it's often true that physicists (and engineers) think they know everything and are smarter than everybody else. Especially in biology/medicine. My brother-in-law, an engineer, is a budding antivaxer/homebirther. My best friend, a physicist, is deeply into ayurvedic woo.
Posted by: woozy | June 18, 2009 9:48 PM
Aren't journals supposed to have editors?Posted by: emote_control | June 18, 2009 9:55 PM
@91: Well, you learn something new every day. Like the quality of the editors at the EPJ-AP.
Posted by: SteveL
|
June 18, 2009 10:13 PM
I'm surprised that a European journal insists on English.
Posted by: Pikemann Urge | June 18, 2009 11:33 PM
AJS #79, you rock dude.
Vincent, you were brave showing up here. I'd say about a quarter of posters are know-it-all ankle-biters. Remember that WB cartoon with the two dogs? The little one was saying to the big one something like "Boy, nobody's tougher than you, George. I bet you could lick 'em, eh George?" and just being really annoying. The big dog got beaten by the Kangaroo I think.
Personally I'm wondering when chaos theory will be applied to biology. That will be sweet as. Or is it already?
Posted by: Samantha Vimes | June 18, 2009 11:51 PM
Fleury has definite crank-like qualities-- it's always worrying when someone says people are too stupid to understand him, rather than explaining anything. Or claiming that any criticism more detailed than, "We already know the real answers" proves he's on to something.
Posted by: Ichthyic | June 19, 2009 1:46 AM
If so, are three pairs of fins early or late in fis-descent terms?
ah, the problem you're having is that only pectoral and pelvic fins are paired.
anal, caudal, and dorsal fins are not.
Posted by: Ichthyic | June 19, 2009 1:48 AM
Personally I'm wondering when chaos theory will be applied to biology. That will be sweet as. Or is it already?
yes.
mostly to growth and development patterns.
easy google; IIRC there are at least 2 popular books on the subject that should pop up on a quick search.
Posted by: Bernard Bumner
|
June 19, 2009 6:35 AM
That being the case, or not, there isn't anything particularly brave about streaking through the place waving your bare arse in people's face and running away.
Normally, when scientists are confronted with scientifically literate criticisms of their work, they feel the need to offer a scientifically literate defense. I can understand that being labelled a crank can be stinging, but if Vincent genuinely feels misrepresented, then his right to reply might have been better used to address the substantial criticisms of the paper. If people misundertand me I personally feel the need to explain, and especially if someone has missed the point of my research.
Remember, people here - whatever your opinion of them - are often professional scientists, and many of us work in developmental biology, cell biology, or genetics. You'd imagine that this exactly the audience that this kind of interdisciplinary research should be pitched to (as well ss biophysicists).
Posted by: vincent fleury | June 19, 2009 7:18 AM
Sir,
it is extremely difficult to discuss with a crowd, which is a mix of scientists and of lunatics.
You are welcome to visit my website, or, better, read some article, and ask me in private any reasonable question. But do not infer anything insulting from anyone who does not feel like entering a debate over here.
Prof. Myers is certainly in himself a nice person, but on the one hand he does not understand the physics questions I discuss, and on the other hand, he himself fleas away and leaves the tap open to any paranoid comment.
Therefore there is no point in "discussing" here, and I read many comments of reasonnable people who seem to agree that there is no way a scientific elevated debate can be held on these premises.
Let me point you to the fact that I sent him personnally a small mail asking gently him, as a reply, to simply put an animation, and a link to a page on brains, which was really not a lot; instead of that, he posted the mail, with some ironical comment, which was not what I asked for.
Therefore, it is obvious that M. Myers has gone as far into his own way as to start to manipulate things and people, probably without thinking that he does hurting and illegal things, against people who do not deserve it and are not even his adversary, an that he shows worldwide how bad his manners are, up to the point that he promotes bad science all the time from some peremptory position.
I am a normal scientist, working in a normal lab, conducting scientific research on embryos at full time, and putting reasonable equations onto developmental phenomena which exists (such as swirling flows in blastulas), and have been known for long ; if his opinion is otherwise, let it be, if it is not, he should be able to understand that the very way this blog is constructed is an endless pour of hatred, even against moderate people. If you, or him, need evidence that there exist vortex flows in embryo development, which were never properly modeled, fair enough, I can give it to you, and you will anyway find it in my papers, but the very fact that M. Myers scorns that is an arrow pointing to the exit.
Most comments above, uncluding Prof. Myers are hurting and for the most, stupid. All this is quite useless, and somewhat revealing.
Posted by: Bernard Bumner
|
June 19, 2009 8:35 AM
I'm afraid that this is simply a consequence of the blog format.
I can see why you would not want to mount a defense of your entire paper on a forum such as this.
However, the function of this blog is to disseminate its author's opinions, rather to provide unbiased, purely educational material. Not that this makes the author wrong or biased, in this case. The point being that, if you really didn't want to use this as a forum to defend your work, then you would have been better served by simply ignoring it.
The one thing that is guaranteed to provoke the ire of the commenter here - or on almost any blog - is to apparently ignore their questions. After all, people contribute to these things because they want their voice to be heard, and feel that they have some important point to make.
An entirely fair point and, actually, not one which is particularly being questioned in and of itself. The substantive criticisms are mainly around; the quality of the manuscript (which is as much a fault of the editorial board, as your own, given that many problems may be ones of translation); some apparent failures to properly integrate molecular and genetic ontology into your discussion; possible overstatement of the importance of early embryonic dynamics without reference to known biochemistry and genetics. It may be that the confusion stems from misunderstanding, or even from legitimate differences in the interpretation of evidence.
Still, many of those things are scientific questions. However, I think that you have made the classic mistake in coming to this blog, of taking something on the internet too seriously. Blog comments always contain a certain element of incivility, and a large dose of misunderstanding. If you choose to engage with commenters, then you also need to be prepared to ignore insults in order to find the questions. Any perceived attempt to dodge or ignore questions will always, and without exception, be met with hostility. That is simply the nature of these sites.
If you wish to avoid invective, then you have to rise above it yourself. Dipping in to mount a half defence, and pour scorn upon commenters will do nothing to improve people's opinion of you.
I think you may find it better for your mood to stop reading these comments.
Posted by: vincent fleury | June 19, 2009 9:04 AM
Anyone at a research level in embryology knows that there exist vortex movements in embryo development, and therefore cannot write :
" Fleury seems to believe development proceeds by swirling forces spinning about in the embryo, and gives us fictitious diagrams like this one..."
simply because development does proceed by swirling forces.
Mr Myers ends his incompetent review by :
"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."
I sent to Mr Myers a link to a page containing about 20 images of such lines, in the form of blood vessels stretched in the growth field. Instead of pausing a little bit and thinking "oh my gosh, maybe we have something there", Mr Myers manipulates my reply and continues on something else.
Conclusion : Mr Myers is a ...... (self censorship), and he is not interested in any way in scientific reasoning. He is only interested in the flow of his blog.
The true problem is not me, my work, my english mispells, my not knowing this or that biological fact. The problem is Mr Myers launching debates from an incompetent point of view, unleashing the mob, and then going away, and letting people think that this is good.
Let me go back to my lab, I am expecting a new batch of embryos,and must clean the incubators.
Posted by: Aquaria | June 19, 2009 11:21 AM
M. Fleury, that's Dr. Myers.
And please cease the ad hominems. It only makes you look like pathetic crank.
Finally, ask yourself this, if you can tamp the swelling of your colossal ego: Is it possible that you might have been entirely wrong about the biology? Is it possible that it is extreme hubris to think that you, with training only in physics, are smarter at biology than someone who has devoted his life to that field of study?
Do you have enough humility and integrity to admit that?
If you don't, then you're definitely a crank.
Posted by: vincent fleury | June 19, 2009 11:49 AM
I am humble in front of reality: the vortices in embryos, which are well known to exist, and which need very tedious work to model, let alone understand,
not in front of authorities.
Posted by: oldcola | June 19, 2009 1:35 PM
@ #103
Come on Fleury,
Your humility consist to say that since 1929 to our days, embryologists who observed gastrulation of the chicken failed to observe two vortices, that you alone have seen up to now. Right? Half your model is built on invisible vortices you have being unable to show the last two years.
And your humility inhibits you to comment on the errors occupying most of your paper. That should be really embarrassing for the people who accepted the paper. And your colleagues. If not for you.
And your humility don't let you dare explain us how you cocked a correlation over inexistent data. #61 above.
The main authority is reality. You fail to acknowledge it.
Posted by: Stuart Pivar | June 19, 2009 6:03 PM
My name came up in the dispute between PZ and Dr. Vincent Fleury over the review of Dr. Fleury's paper on embryogenesis by self-organization. In the past, my work has been questioned and criticized severely. The scientific criticisms are addressed in a new, expanded book ON THE ORIGIN OF FORM distributed by Random House. Please see www.ontheoriginofform.com.
Posted by: vf | June 20, 2009 1:38 AM
The four domains of revolution were evidenced by at least 3 different labs : Kees Weijer et al in Dundee, E. Farge et al. in France, Zamir et al. in the US.
At least you seem to acknowledge that there exist certainly 2 of these vortices, as known since 1929, indeed. That is a progress over mr Myers. Please let him know, he lags very much behind, and so do most of the people commenting here.
For the rest, especially the role of FGF10 in lung development, see my website or papers. A function satisfying F(x)=-F(-x) and F(2x)=2F(x) is linear.
The methods used by internet users to discuss are self-destructive.
Posted by: cygnus | June 20, 2009 2:39 AM
M. Fleury, that's Dr. Myers.
To be fair, that'd be Dr. Fleury as well. He is French and the cultural use of honorifics vary country to country.
Is it possible that it is extreme hubris to think that you, with training only in physics, are smarter at biology than someone who has devoted his life to that field of study?
Again, to be fair, academics, even the sciences, often fall into fads and politics and pig-headedness. I imagine all departments have a few fossils kicking about th whom even high-school kids know more.
What we have here is an outside academic getting a, mostly likely deservedly, scathing review from an expert in the field who blogs about it, the outside academic getting a bit pissy, which is kind of thin-skinned but not surprising; scathing reviews do hurt, all being witnessed on a blog by fans who are engaging in anything other than "peer-review".
Fleury may be dead wrong and utterly ignorant (although I'm only taking the biologists' here word for it; -- I'm in absolutely no sense either of the gentlemen's peer) and a bit ad hominem pouty (well, "pissy" seems a more accurate description) but this really is more of a case of an academic pissing contest (in which case, Fleury's woefully out of his depth) then a case of a whacko crank.
Posted by: Joel Klinepeter | June 20, 2009 3:00 AM
I'm curious about something Dr. Fleury. I took the time to look at the animations you provided in one of your comments, granted I couldn't read the captions as I have very little skill with any language other than my first one (on that note I can empathize with trying to write a paper in a language that isn't native to you). Viewing these animations I can certainly see what you're trying to portray, however they left me with a fundamental question...
With the nature of evolutionary development (largely gradual change over time) it seems to me that when viewed in hindsight any genetically driven morphology could be broken down into warping patterns such as you portrayed due to the nature of changes caused by selective pressures (environmental factors driving natural selection). In the case of the skull I'm curious what experimental data there is to show that the morphologies present are CAUSED by the physics principles that you are arguing for. Based on my understanding of biology (granted there's more that I don't know than that I do know) it seems more likely that the morphologies CAUSED by genetics and natural selection can be seen to REFLECT these particular physics principles.
That is to say, with the human propensity to see artifice and patterns in the world around us it seems more likely (to me at least) that the observed vortices are a byproduct of the morphological pattern driven by genetics, hormones, and other aspects of molecular biology.
I am always willing to be shown that I am wrong (how else can we learn after all) and as such I would truly like to know if your data only shows that these vortices can be observed and could therefore be a byproduct of the morphology, or if your research shows definitively that the morphology is CAUSED by these vortices.
Posted by: oldcola | June 20, 2009 3:48 AM
@vf #106
The question is how do you verify that this is the right function without data, try to explain that simply to us poor biologists living in that terrible darkness you see around us:
- a single measure (control/test) for an assumed ∆P (assumptions varying between 3 and 2 times zero! Your words, your slide on a public conference)
And by single measure I mean really a single one reported in the paper (1) (thus unknown variance), for a single Fgf (Fgf10)
(1) doi:10.1016/j.mod.2007.10.013
The four domains evidenced? You really have problems with number VF:
doi:10.1016/j.ydbio.2006.04.451Zamir et al. don't address the question. doi: 10.1073/pnas.0606100103
Farge et al.? Maybe a reference, at least a doi?
@cygnus #107
PZ describes quite well the paper:
blah balh hlab blah lhab, tagada, ta-dah
No typos here, just errors from Fleury.
Tagada being the wrong conclusion driven from wrong inputs.
Ta-dah, a model with no connexion to reality (at least yet and that's almost 2 years we wait for Fleury to show us an image of the four vortices his model claim).
A pissing contest you say. Let's take it that way. EPJ AP pissed in the soup by accepting the paper at its current state. And so have done Fleury by submitting.
Nobody likes piss in his soup.
I first challenged him to publish his theory, in a scientific journal, on January 17, 2007. He submitted the paper on June 10, 2008 and it wasn't accepted before January 26, 2009. Three years later; plenty of time to prepare something without blatant errors on the biology-side. Or gratuitous assertions (which don't stand by any standard).
Wrong premises, wrong conclusions, or to put it in a more bloggish way, BS in, BS out.
Posted by: oldcola | June 20, 2009 3:55 AM
Two years later, I'm getting infected with VF's problems :-)
Posted by: vincent fleury | June 20, 2009 4:34 AM
I understand your comment. My paper deals mostly with this question, especially by the end.
The point is better understood on a melon :
a melon is round, the roundness of a melon is caused by genetical facts (turgor pressure), however, the shape "melon" is spherical. You can write the equation of this form as "set of points at distance R of the center", that contains no genetics at all.
In the case of a tetrapods, you can write : Tetrapod=time integral of a dipolar flow. The difference between tetrapods and melons is that the driving force of melon growth is turgor pressure (a monopole) while the driving force of tetrapods is cell migration (a dipole)
That contains no genetics. How come?
it is because all genetic parameters map onto a physical field of deformation, and the genetic products apply onto prefactors of a dimensionless vector field.
The set of possible deformations is much reduced as compared to the set of genes. It is not bijective.
The existence of a dimensionles vector field is best understood by taking the example of parabolas in gravitational fields : if you throw a stone, all trajectories are parabolas. If the stone hits a head you can say : the blow was determined or "caused" by the fellow who sent the stone. But you can as well say : it is determined by the fact that the gravitational field has this specific mathematical form (Newton's law). You have a general law, and the parameters. By selecting parameters, you elicit one of the forms inside the spectrum allowed by the general law.
On all planets, all thrown stones will have a parabolic trajectory, whether they are made of quartz, limestone, or chalk.
A similar situation exists in tissue development. Final shapes are the cross-product of an initial symmetry breaking, by a slow creeping flow, (Stokes flow). All this is explained in detail in my paper.
You can say "I disagree", you cannot say it is tautological and "nothing". It is hurting and low, and by the way, stated by "a person" on a personal blog, not by an abstract ectoplasm, therefore I can certainly analyze this behaviour in terms of person; this behaviour is very much revealing about Prof. Myers himself.
And one can imagine at once all sorts of interesting experiments around these issues. It is all too comfortable to say "there is nothing".
For the specific case of the skull, how the dimensionless field is constructed by previous flow of the blastula is explained in the paper (U turn folding of the neural crest during von Karman buckling : just flex your elbow and look at the folds of your shirt)
that the brain expands by mechanical force has been evidenced for long, there are historical papers in the 70's on this question, and also a long line of papers on microcephalia, and related conditions with increased skull size (hydrocephalia etc.), also, there is a long line of work on cortical convolutional development (brain folding), and its link to in plane cortical stress.
For the evolutionnary issues, there is a long line of work in the last 20 years about the correlated anatomy of skull expansion vs jaw recession.
Finally, I myself investigated the orientational order present in brain vesicles and its relation to the growth field, you may find on my website relevant images and publications.
I treat these questions with physical vector fields, in my paper there is an entire section devoted to alternative views and how to make a synthesis of the two. Prof. Myers says there is "no synthesis", while I do painstakingly try honnestly to address the marriage of these issues, and it is probably the first time this is done so far. Prof Myers statements are defamatory. I do not know why somebody like prof. Myers should feel happy with such defamation.
I have no reason to be is adversary and he has nothing to fear from my work.
If we meet I expect that he will pay the drinks.
Posted by: vincent fleury | June 20, 2009 1:04 PM
Oh, still insisting about the 4 vortices;
you may find the evidence and references at:
http://www.msc.univ-paris-diderot.fr/~vincent/englishEnresume3.htm
please contact Mr Myers to reach together an agreement about these vortices, he thinks they do not exist, and then we can restart any civilized discussion, but he seems very much busy with other things.
concerning the lung development, it is well known that lung development is linearly related to pressure (plesae do pressure lung expansion, diaphragmatic hernia on google or pubmed), both towards high pressures and low pressures, around the physiological case and it is well known that clamping the trachea provokes a doubling of pressure inside the lung duct (please type trachea occlusion). It is also well known that the growth factor for lung expansion is FGF10 (FGF10, lung). You mention that I state that I did not measure the pressures myself, so you see, I am not hiding anything, and trust other people's data. Nevertheless, following existing work of others, in our clamped lungs the pressure should be doubled, and if it is, the lung expansion should be doubled. The lung expansion is indeed doubled. So that's it.
I am not sure whether the relevance of physics to pattern formation of lungs relies heavily on whether the mechano-transduction of FGF10 is linear or not, but whatever the exact law, the overall result (the expansion force, eventually), is linear in pressure, so even if in some limiting case the regulation of FGF10 is (resp.) superlinear or sub-linear (what is your own evidence by the way?), some resp. sublinear or superlinear regulation via the pathway of FGF10 must appear to just precisely cancel any non-linear régime, which we do not see (and it is anyway useless, since what matters is the morphogenetic effect, not the detail of the mathematical form of each step in the pathway) , and can be dismissed at least by Occam's principle. So any evidence so far demonstrates that FGF10 is linearly regulated by pressure, but any new evidence will be welcome.
Posted by: cygnus | June 20, 2009 4:02 PM
oldcola: # 111
@cygnus #107: PZ describes quite well the paper: blah balh hlab blah lhab, tagada, ta-dah
It's very true. He did describe the paper well, and I take his word on it that it is garbage and that the idea that forms arise from physical properties to tissues have been discreditted for decades.
I was responding to the comment that it was "hubris" for a physicist to even attempt a paper on biology. Yes, I agree that when one is limitted in a field one should really do one's research before diving off into a 51-page paper on a vastly discreditted theory. And yes, I agree, that when one's paper get publically scathed and discreditted it'd probably be isn't politic or smart to get huffy and pissy and prickly. But I balk at the idea that acedamics shouldn't challenge other academics. Yes, it'd be hubris (or more often delusional crankiness) to then reject all peer-review and insist you are right and the entire world of biology for the last fifty years is wrong. But I'm loath to call it "hubris" just for publishing (even when its whacko publishing garbage).
A pissing contest you say. Let's take it that way. EPJ AP pissed in the soup by accepting the paper at its current state. And so have done Fleury by submitting.
Nobody likes piss in his soup.
Hey, I never said a pissing contest was a bad thing! And I never said PZ started it. And I definately did say PZ was winning it. Pissing contests are an inevitable part of academia.
My point in refering it to a "pissing contest" was to distinguish it from the more common (and fun) "turkey/creationist shoot". In a pissing contest we can whip out our expertise and pedigree and pee at will, but only those expertise and pedigree (that's PZ and you but not me) should engage in the whooping and smacking and making fun of bad grammer we all get to engage in the turkey shoot whack-offs.
(My terminology is tongue in cheek. I enjoy a good whack-off. And I'll compare my piss to the best of you in subjects I know about or in general debate.)
I first challenged him to publish his theory, in a scientific journal, on January 17, 2007. He submitted the paper on June 10, 2008 and it wasn't accepted before January 26, 2009. Three years later; plenty of time to prepare something without blatant errors on the biology-side. Or gratuitous assertions (which don't stand by any standard).
Well, you are certainly qualified to dismiss his results. I wasn't defending this guy I'd never heard of before-- just pointing out fairness where fairness was due. (example calling PZ "Mr. Myers" as is the french custom.)
Posted by: vincent fleury | June 20, 2009 5:40 PM
I was asked mean questions about the regulation of FGF10 by presure during lung development, hereafter is a reference for the fact that clamping doubles pressure :
Pediatr Res. 1998 Feb;43(2):184-90. Links
Stimulation of lung growth by tracheal obstruction in fetal sheep: relation to luminal pressure and lung liquid volume.Nardo L, Hooper SB, Harding R.
Department of Physiology, Monash University, Clayton, Victoria, Australia.
a reference about linearity of growth with pressure
J Appl Physiol. 2001 Feb;90(2):493-500. Links
Fetal lung growth after short-term tracheal occlusion is linearly related to intratracheal pressure.Kitano Y, Von Allmen D, Kanai M, Quinn TM, Davies P, Kitano Y, Flake AW.
The Children's Institute for Surgical Science and The Center for Fetal Diagnosis and Treatment
a recent review for anyone interested in how pressure controls lung expansion:
Am J Med Genet C Semin Med Genet. 2007 May 15;145C(2):125-38. Links
Tracheal occlusion: a review of obstructing fetal lungs to make them grow and mature.Khan PA, Cloutier M, Piedboeuf B.
CRCHUL Medical Research Centre, Laval University, Québec, Canada.
Fetal lung growth and functional differentiation are affected strongly by the extent that pulmonary tissue is distended (expanded) by liquid that naturally fills developing future airspaces. Methods that prevent normal egress of this lung fluid through the trachea magnify mechanical stretching of lung parenchymal cells, thereby promoting lung development. Indeed, experimental observations demonstrate that in utero tracheal occlusion (TO) performed on fetuses during the late canalicular-early saccular stage potently stimulates pulmonary growth and maturation. In this review, we present the four principle non-human animal models of TO/obstruction and discuss them in relation to their utility in elucidating lung development, in remedying congenital diaphragmatic hernia (CDH) as well as in investigating the stretching effects on growth and remodeling of the fine vasculature. (c) 2007 Wiley-Liss, Inc.
the in situs of FGF10 regulation by pressure can be found at
http://www.msc.univ-paris-diderot.fr/~vincent/englishthemeorganes2.html
Posted by: Oldcola
|
June 21, 2009 10:33 AM
Dr Fleury,
Thank you for your comment, it helps me greatly to make my point.
I asked a quite precise question about an assertion in your EPJ AP paper:
and the reference you provide to support it:which redirect the reader to one of your papers to get evidence supporting your assertion.I chosen this particular example, between many, for two reasons:
- it is equally accessible to scientists of any discipline, and every level,
- it is quite simple to explain the problem it presents to a layman.
My point is: no data, no false assertions please.
The simplest way to respond directly would be to provide a list of pressure measurements (which you don't have) and corresponding measurements of fgfs or other growth factors (which you don't have), to a) first establish the correlation, b) the show that it is linear and c) finally, a try to explore if pressure is driving the increase of fgfs expression and not that fgfs over-expression drives the pressure increase, transforming the correlation to a causal relation.
You don't have the data, you submitted a paper including at least this false statement, you spend your energy and use our patience trying to indirectly support what you presented as a "fact".
You provide one more example of the way you deal with data in your last comment (#112):
"Should be doubled" would never replace a measure and "the lung expansion should be doubled" make the case worst.Your assertion concerns gene expression regulation, not lung expansion, this is the third time you try to give a response considering some other feature.
My point here is not to discuss lung development or fgf expression levels in relation to any varying parameter, but the way you build your point of view on the basis of fragmentary, if not inexistent, data, which don't frankly support it - if one digs a little bit.
And why it may be advisable for any audience, not just biologists, to send it "down the drain", until substantial evidence is provided.
This include people not accustomed with the biological topics you deal with, the audience to which you address your paper, as you said physicists. If you want to teach them something about biology it would be preferable to provide them facts (or at least tag your hypotheses as such) and avoid the errors that constellate your article and have gone under the radar of the review process of EPJ AP.
By referencing your paper you misrepresent your results, but the same is true for other people results you presented, in your paper and in the comments above. For example the case of Weijer at al. (#106) who observed, shown and claimed the presence of two vortices on the chick's epiblast during early steps of gastrulation (a long known feature), which you use as evidence for four of them!
I have already seen your drawings and how they evolved during the last two years and I certainly know that for the moment you haven't provide any evidence of four vortices.
Your drawings are certainly not evidential proof supporting your hypothesis. As an experimentalist, you claim you are, you must easily understand that.
A few years ago I had the bad experience to struggle to separate facts from misrepresentation of reality in your first publication of your gastrulation model and spent a lot of time to come to the "down the drain" conclusion, despite my first positive impression. You helped me greatly at the time by being insistent on disconnecting physics and biology, trying to downplay the role of genetics and redefine biological evolution your way.
I don't think many people will try to do so with the lengthy and lousy introduction you provide for the paper reviewed here (I'll do so as I promised you).
Many may be willing to accept it coming from a fellow physicist, whom they will naturally trust. And maybe they will join you mourning for the poor condition of biologists, wandering into darkness, not even knowing where the lateral mesoderm plate comes from, satisfied with in vivo competition essays with just 10% positive results.
And probably you expect that many will celebrate the genious physicist that at least grabbed the meaning of all that and is ready to teach it to the whole world, even those poor biologists. With all due humility.
You should first learn how to express an hypothesis with no supporting evidence (certainly no as a fact, going into specifics), learn where the lateral plate mesoderm comes from, learn that two is not evidence for four, learn to not misrepresent other peoples results just to make them support your point of view.
By making a general audience point on the way you deal with reality (badly), I hope your fellow physicists will become suspicious of other assertions you presented - and they haven't (can't) check, being outside of their sphere of competence.
Maybe a detailed review by an embryologist for the benefit of EPJ AP editors would be recommended if they want to maintain the paper.
Anyway, they will have to publish a long, long, errata list.
Posted by: Oldcola
|
June 21, 2009 11:13 AM
@ #113
Hi cygnus,
I was trying to make a point and your comment and reply helped a lot I think to induce Fleury's reply.
I hope that my previous comment (#115) makes clear that this is not just a pissing contest of academia peopl , but but the evaluation of the method Fleury use to access and discuss and model reality, which can't be really be qualified as scientific and except serendipitous coincidences is due to fail.
Fleury's paper isn't really important, Fleury's method is *the* problem and this is accessible to non specialists of the discussed domains, including you. ;-)
Posted by: vincent fleury | June 21, 2009 2:19 PM
You are welcome to send any comment to any journal above about these issues, I will gladly reply.
It is absolutely obvious from all references I have given to you that there exists a saddle-point separating the embryo blastula into four domains of revolution during formation of the flanks, it is modelled in my papers, even before it was recognized, and explicitely stated in such papers as Kees Weijer's et al. (and also private communication). If you do not understand this you should do something else. Anyone here, who is a scientist, will obviously see the saddle-point on all recent images of gastrulation in tetrapods. If you don't see it, please ask a colleague around you to help you.
By the way, did you inform Prof. Myers that there are vortices on blastulas? He should be informed urgently.
Concerning the FGF10, it is all too clear that the existing evidence demonstrates that the regulation by pressure is linear. That can be obtained by simple logical deduction, and by the existing data, especially ours, and the references contained in the paper. This can certainly be debated, and you are welcome to provide other data.
You really should stop, you are making a fool of yourself.
Posted by: Oldcola
|
June 21, 2009 4:45 PM
I'll address a list of errata to EPJ AP, you can find them here and start preparing your reply and maybe post it in the comments. I hope you informed Dr Drévillon already about those horrible, trivial, errors that constellate the paper.Are you sure, really sure that there are four vortices and still unable to show them? Because you badly need those two invisible vortices.
By the way, I will not try to teach an embryologist embryology, do it yourself. It could be funny.
Concerning your assertion I hope I made it clear it is false. It's not upon me to provide data other then the fact that you don't have enough to support it. I've done so and you greatly helped; thank you for that.
There are other foolish people around, foolish of my kind I mean, and I very much like to know I'm not alone in my condition.
Should prepare a post to acknowledge their comments.
Posted by: vincent fleury | June 22, 2009 3:48 AM
@"For example the case of Weijer at al. (#106) who observed, shown and claimed the presence of two vortices on the chick's epiblast during early steps of gastrulation (a long known feature), which you use as evidence for four of them!"
@"Are you sure, really sure that there are four vortices and still unable to show them? Because you badly need those two invisible vortices.
"
Sir,
it is all explained in detail in this page,
http://www.msc.univ-paris-diderot.fr/~vincent/englishEnresume3.htm
which contains the actual images, and the references.
Kees Weijer and coworkers show explicitely the hyperbolic flow, with the four domains of revolution, separated by a saddle-point, which is explicitely evidenced by themselves in the figure and paper (C. Cui, X. Yang, M. Chuai, J. A. Glazier, C. J. Weijer, Dev. Biol. 284, 37 (2005). Nota Bene : the red square "circling" the said saddle-point is by them) and it is duely quoted in the EPJ paper (incompetently reviewed by Mr Myers, who seems sadly to be unaware of the existence of these vortices).
If you are unable to see this, and the confirming data obtained later on by other groups, you are either seriously impaired mentally, or unable to follow any scientific reasoning.
Let anyone who is a scientist judge by himself, but please stop this trolling now, and these defamatory comments.
I understand that this is a chock for all main stream biologists, and that Dr Myers may take some time to make up his mind, but it is time for change, and defamation will only retard the diffusion of these facts.
Posted by: vincent fleury | June 22, 2009 4:54 AM
For people still interested, the original paper reads :
"the red box indicates the saddle-point area where the cell flows merge and bifurcate along the antero-posterior direction"
Our experiments showed clearly that the cells flowing towards the streak bifurcate into two streams that flow either anteriorily (contributing to the posterior extension of the streak) or porteriorily (contributing to the posterior extension of the streak). Thus streak elongation is bidirectionnal from its initiation.
(NB : two streams on each left and right side of the embryo=4 streams).
Anyone who ever thought that animal formation is oriented antero-posteriorly should revise its conceptions. Including Mr Myers. Tetrapods are formed bidirectionnaly from the saddle-point (presumptive navel) towards the shoulders and towards the pelvis, with mirror symmetry, by a hyperbolic flow (saddle point), with 4 revolutions organized around a stagnation point.
And basta.
Posted by: Oldcola
|
June 22, 2009 10:34 AM
@120
You need, for your model, Dr Fleury four vortices not four streams, right?
To describe the cellular flows you displayed in your website and reported over the chick embryo.
Maybe you changed your mind and you didn't said so? Could that be possible?
Posted by: vincent fleury | June 22, 2009 11:56 AM
Vekris (Oldcola), you don't understand a shit of this problem.
It is the same thing THE SAME THING. There aren't "4 streams" you do not even know the proper wording. You are just like Myers, a peremptory pedantic ignorant who scorns without knowing anything, for fear of loosing ground and being overtaken: it is a single flow called "hyperbolic" flow which has four domains of opposite windings, around a stagnation point (presumptive navel). The hyperbolic flow is the mathematical linearization of the addition of four vortex flows induced by two dipoles head on. The streamlines (curves tangent locally to the flow vector) in each domain close upon themselves in the form of vortices, which may be complete or not so complete it does not matter, it is because of the boundary condition : the stagnation point is quite low in the blastula (see your navel). Will you ever understand this or are you a true manipulator?
It has always been formulated like that in my papers, it is explicitely stated at length in the 2006 paper in Revue des questions scientifiques : that the vortices need not be complete, and that animals with only two large vortices will not have hindlimbs; that early animals will first have forelimbs and next forelimbs and hindlimbs; all this and the pattern of the blastula with incomplete vortices is already in the 2006 paper, and in my book in 2006 (all submitted 2005) the relevant figures like
http://www.msc.univ-paris-diderot.fr/~vincent/Enresume3_fichiers/image017.jpg
are found in several papers I have written, like
Vincent Fleury, La mathématisation complète d'un vertébré s'avère possible, Revue des Questions Scientifiques, N°177 (3-4): 235-278 (2006), or the EPJ review
You do not need a full rotation to generate a limb : a partial winding suffices to lift the tissue. Think of a beaker which turns, if you turn 1/4th of a beaker, for 1/4th of a revolution, the surface of water deforms also inside 1/4th of a beaker for 1/4th of a revolution, it is not a matter of streamlines making complete loops, it is a matter of local stresses. Your hatred is turning you nuts.
In addition, the embryo does not form from the entire blastula, it forms from a central part of it, even the vortices above the navel do not end entirely inside the embryo. Cut off an elongated rectangle in the center of the blastula, and you have even a more symmetrical hyperbolic flow around the presumptive navel.
Now, if you do not understand this and continue to defamate me on this blog or on your blog, or all the others which you wasted tour time to open against me, I shall take legal steps. I mean it, and you know it.
It took you 2 years to at last admit that there are 4 domains of revolution, everybody since Wetzel in 1929 is wrong, and nobody noticed it until my paper, it is just true, you have just admitted it implicitely by your comment.
Now do one step more, and you have the explanation of the origin of tetrapods, for G*d sake.
And please, I mean it, now that thanks to me you know all this so well, make me the favor of explaining all this to your mentor (the big-moustache ignorant) and to all the pityful biologists who insult me on this premises.
Vekris : the antero-posterior construction of animals is bullshit, the induction of limbs by genes is bullshit, the colinearity of hox genes is bullshit, the selection of tetrapods by evolution is bullshit, the duplication of genes between hindlimbs and forelimbs is bullshit
and you now know it, better than anyone else.
And please withdraw the lamentable youtube movie that you issued, and close all your stupid websites opened against me and my work, and please shut up now.
Posted by: Oldcola
|
June 22, 2009 12:04 PM
…
Posted by: TheBlackCat | June 22, 2009 4:10 PM
The moment someone threatens legal action during a supposedly scientific debate they have lost. At the very least they have lost all credibility. No matter how ugly they may get (and this is pretty mild compared to some debates I have seen), threating legal action to silence your opponents is never justified in science.
Further demanding that someone take down all online material critical of you work just sounds like wounded pride.
And then you ask us to reject essentially everything we know about development.
I honestly considered what you are saying interesting and I really had some suspicions that some of this may have merit. But you started acting like this, insulting and dismissing your critics, throwing out large bodies of strong evidence as "bullshit" without justification, demanding that your opponents stop criticizing your arguments and methodology, and threatening legal action if they don't. That's not science. That is not how scientific debates are done.
Your idea may have merit, they really might. But it doesn't really matter anymore. You've lost all credibility to me. I simply can't trust anything you say anymore. I can't trust someone who thinks the proper way to deal with criticism is to threaten legal action. All that means to me is that you are incapable of dealing with criticism. And if someone cannot deal with criticism, it means that person is taking his or her work too personally and thus also cannot be trusted to look at it objectively.
Posted by: TheBlackCat | June 22, 2009 4:18 PM
I also found this quite ironic:
From post 120:
And then from post 122:
Posted by: vincent | June 22, 2009 5:41 PM
you do not understand :
Mr Oldcola has opened about 5 blogs in France against me, he has sent anonymous copies of stupid comments of my work to my hierarchy, he has opened blogs taking my name on several providers, he contacts students before my courses to defamate me etc. he has already been gently asked to withdraw from several forums.
I am a civil servant of the french government, under legal protection explicitely against him, and he has had already to withdraw several pages containing all sorts of insults like ass hole etc. against me on his personal web pages. etc. etc.
He has sent my paper to Myers asking him to review it, in order to be able to use this blog of Myers as aircraft carrier for his defamation.
It is not what you think. Be careful with external appearance of things, and thanks for reading, I was not even thiking anyone was still following this stupid discussion with this man.
@TheBlackCat
you did not notice : I was reproducing the words of Weijer who is not himself a hydrodynamicist either; those not accurate words were not my own words.
You see, things are not the way they appear at rapid glance
Good luck
Posted by: vf | June 22, 2009 6:00 PM
this internet thins are derisory
Posted by: vf | June 22, 2009 6:01 PM
these internet debates are derisory, who can feel happy with all this?
Posted by: Oldcola
|
June 23, 2009 2:36 AM
@ 126
He has sent my paper to Myers asking him to review it, in order to be able to use this blog of Myers as aircraft carrier for his defamation.Nope, I wanted an expert's opinion on this stuff. You already complained that your papers were rejected several time from biology publishing journals, and PZ's review is a public display of what a biologist reviewer could reply.
No news that I'm opposing your theory (for people over here this is news), no news that I urged you to publish it in a science journal so the criticism could be addressed to the published content (and they are), and I'm happy that other people share my opinions about the content and the way you think a scientific dispute may be concluded.
Maybe I'm stupid, but you are the one unable to answer specific questions: e.g. (#61) about the content of your paper. You think you answered in an appropriate way, I think you don't, other people have what is necessary to make their own opinion on that.
It would be much better if the paper was published in PLoS ONE (that's what I proposed), so the comments would be more sciency.
I never said you are an asshole! The post concerning the way assholes deal with science related discussions bringing in their supernatural beliefs as soon as rationalism deserves them is still on display. Four posts I withdraw because I didn't wanted to pay a lawyer to be sure that they were OK. I'll do that.
The fact that you are "a civil servant of the french government, under legal protection" don't dispense you of doing good science, neither can protect you against substantiated criticism of your paper.
Maybe you would be happy if it was so, but in front of your peers, including those being "civil servants of the french government", you should try to justify the errors constellating your paper. The list is available and the comments open.
Posted by: Oldcola
|
June 23, 2009 2:39 AM
argh ! bad formating, should use "preview" option more often :-(
Posted by: vincent fleury | June 23, 2009 5:41 AM
You have admitted above that there are 4 domains of opposite (2 clockwise, 2 anticlockwise), revolutions of flows in a tetrapod blastula, centred on the presumtive navel, after 2 years of blindness
4 revolutions - 4 limbs what a coincidence
All the rest is derisory and pityful, and the fruit of your unability to see this in the first day, you can continue your masquarade, with whoever you want.
Do not forget to inform Myers, he should teach that.
Sorry chaps (if any!), I leave, now that the case is made; please just follow all the links given by this man, all the way down.
You were right Blackcat, there is no need to remove the critical pages, let them stay there.
Posted by: Oldcola
|
June 23, 2009 8:49 AM
Vincent Fleury
It may be easy to falsely report one's paper with imaginary content, it is much more difficult to do so here.
Now, read attentively, take your time to think about it and make your mind:
Let me translate it for you so the language barrier wouldn't impair understanding:
If you understand that this is an acknowledgment of
you have a quite serious problem to deal with.And on that I can't help you.
Posted by: Stephen Wells | June 23, 2009 9:07 AM
If cells move in ways that can be described as a vortex, that does not mean that cells move that way _because_ a vortex is moving them. Fleury's entire argument thus fails at the start.
Posted by: Oldcola
|
June 23, 2009 11:29 AM
@133
You are rights Stephen, this is the first layer problem: Fleury's assumption is that embryos behave (maybe more then behave, are?) as liquids.
Posted by: TheBlackCat | June 23, 2009 11:55 AM
If you can't deal with the critique of an expert in the field, that says more about you than it does about anyone else. I was following it because I was hoping, since you kept commenting despite your repeated claims that you weren't going to, that you would eventually get around to responding to the numerous substantial criticisms that have been made here about your work. Unfortunately you have not done so. Instead you have cherry-picked the criticism you respond to, focus on an inconsequential debate about details of the idea while ignoring more important and more fundamental problems people have pointed out with your work.To put it simply, you are getting way ahead of yourself. You are debating the details of these supposed vortexes, but the details are meaningless if the fundamentals are not there, and you have so far ignored all criticisms and questions regarding the fundamentals (and not just by oldcola, but by many commenters here).
Further, your work was not published in a subject-appropriate journal. This has allowed you to bypass review by experts in the relevant field (developmental biology). I am not sure the reason. So far the only ones I can think of are that you thought a physics journal would be more appropriate, which it most certainly is not, or that you either tried and failed to get it accepted in an appropriate journal or did not think it would get accepted to begin with, in which case you should have addressed the problems with the paper that prevented or would have prevented its acceptance. Your choice in publishing venue is very worrisome.
Further, you addressed at length your experience working with embryos, yet so far have not provided any indication that you are familiar with the substantial research on the subject by others. For instance your lack of knowledge of the lateral plate, which even I knew (and I barely have a biology 101-level understanding of development), does not bode well for your understanding of the field (which is completely independent of your experience working with embryos).
To make a comparison to your field, if someone had told you they had worked with flowing water a lot, but did not seem to understand the principle of shear stress, would you have much confidence in their expertise in fluid mechanics? Would you trust their claims that they have single-handedly overturned essentially the entire field of fluid mechanics, and would you think very highly of the person when he or she dismissed all the fundamental principles of fluid mechanics as "bullshit"?
Imagine, for a second, that this person's idea is that a fluid's properties are determined by small particles suspended in the fluid and that the fluid itself is unimportant. The person does establish that at least in some fluids that there are particles suspended in it (I am not clear on whether you have established the existence of the vortexes or not, but I will grant you that for the purpose of this metaphor). The person hears a lot of criticism of this idea, but focuses his or her discussion on a debate about the shape and size of the particles in one particular case without first establishing a causal relationship between the properties and the particles. Further, the person ignores questions about how the particles could result in substantially different behavior and ignores situations where the particles have been changes but the fluid properties remain the same. The person says that nobody has explained some basic principle of fluid mechanics despite the fact that it is in every basic fluid mechanics textbook and is even taught to in some introductory physics courses. The person dismisses alternative explanations that have been heavily-studied and shown to overcome the problems brought up in his or her idea, the person cannot cite any fundamental problems with the alternatives, does not demonstrate much understanding of the alternatives, yet still dismisses them all as "bullshit". And in the end the person publishes the article in a journal of soil geology, which does deal with particles but where nobody on the journal has any experience with fluid mechanics. The person also appears prone to fits of anger, or at least what looks like anger in print, and threatens legal action against a critic.
Based just on that, how would you judge that person's work? That is all you have to go on, as it is all we have to go on here. Would you be inclined to look much further at that person's work? Would you be willing to give that person the benefit of the doubt, ignore the opinions of experts in the field on his work, and think that you, who knows very little about fluid mechanics or particles, would be in any position to judge the work? I know you know a lot about fluid mechanics, I am asking you to look at what has happened here from the perspective of someone who doesn't (frankly I know more than many, I have studied it briefly, but I also know enough to know I have no clue what you are talking about, and I also don't know nonlinear dynamics).
Look at it from the perspective of an outsider. How would such a person view such an exchange? Because what I just described is exactly what I have taken from this discussion. It may not have been what you were trying to do, it may not have been how you saw it, but it is what I saw, and that is unfortunately all I have to go on when making a decision about whether to pursue the matter any further.
Posted by: vincent fleury | June 24, 2009 2:51 AM
Checking the level of these guys; oh dear!:
the cell-tissue-blastula flow is just the writing of Newton's law. Cell move by cellular traction. They are not poltergeists, they do not teleport. "Viscous materials" is just the name given to materials which move under stress, it is used by everybody in the field to analyze cellular flows.
The integral of the cell tractions is the vortex flow.
Inventing distinctions between vortex streams etc. is derisory. You certainly do not qualify as "peers", neither does PZ. Myers.
I understand that freedom of speech consists in letting these forums be. So pityful.
Posted by: TheBlackCat | June 24, 2009 9:45 AM
Thank you very much, Dr. Fleur, for proving my pointing.
Posted by: Bernard Bumner
|
June 24, 2009 10:14 AM
I almost find it hard to believe that the the last three (or so) posts are the genuine sentiments of Dr. Fluery, and not either an attempt to be deliberately provocative, the work of an imposter, or something that has simply been mangled in translation.
The level of arrogance, bluster, and scientific chauvinism is baffling. I'm surprised that anybody calling themselves a scientist would be willing to casually dismiss huge bodies of established evidence as bullshit - it was embarassing enough that he wasn't willing to embark on a greater synthesis of the fields, let alone to wave them away with the implication that they were simply wrong. But this seems to be exactly what he has done above - unless I've completely failed to follow his point.
I'm still struggling to understand the basis for his theory, and he doesn't seem willing to offer any better explanation of it than is contained within his papers. I've read and reread the paper, and followed the link he gave, and I'm still struggling to follow his point. The paper is not useful, because it doesn't explain most of the points raised here - which is exactly why they were raised here.
I understand at least the general principles of what he is proposing, but can see no basis for it in established genetic and molecular ontology, except as a relatively trivial observation (but only in some aspects of what he describes; I'm not convinced that his model is based only on observation, and that there isn't a great deal of supposition).
Possibly he is approaching this observation with some more sophisticated modelling to describe the system, but he also seems to be extending this to imply causation (whilst dismissing known genetic and molecular explanations). I'm actually not sure, because in his attempt to defend his work, he seems only to do one of two things; tell questioners that they are stupid, or else refer them back to the paper.
An important point is that the paper is not clear in its claims, is not clear in distinguishing data from interpretation, and does nothing to incorporate well-evidenced ontogenic mechanisms (despite needlessly regurgitating a deal of literature concerning exactly that).
He also claims not to want to enter into a scientific discourse on this blog, but instead feels the need to return here to defend himself in the worst and most ineffectual manner possible.
If these comments are indeed his work, then he appears to be a very unhelpful, arrogant, and paranoid individual.
Posted by: slpage | June 26, 2009 10:26 AM
Vincent writes:
"That really is the issue, you need a physics force to generate these bumps [in the lateral plate mesoderm], by fundamental laws of nature (this is what physics means, by the way)."
Could not these bumps be produced by differential cell growth within the tissue brought about by differential concentration gradients of growth factors?
Posted by: slpage | June 26, 2009 10:32 AM
Vincent:
"You certainly do not qualify as "peers", neither does PZ. Myers."
I am a biologist. You are not my peer, Mr. Fleury.
And it shows.
Posted by: Mike Saelim | June 26, 2009 12:11 PM
As a physics graduate student, the first thing I did when I read Fleury's assertions was to laugh. But then again, I've had a good biology upbringing. Please don't let him influence your opinion on physicists - to most of us, he would be considered a crank.
Posted by: slpage | June 27, 2009 9:25 AM
tis himself:
"That's what happens when a biologist ventures into economics, he gets just part of a definition."
And when a non-biologist ventures into biology, what do you think usually happens?
Posted by: slpage | June 27, 2009 9:25 AM
tis himself:
"That's what happens when a biologist ventures into economics, he gets just part of a definition."
And when a non-biologist ventures into biology, what do you think usually happens?
Posted by: dephlogisticated | July 2, 2009 8:06 PM
Fleury and Pivar must not know about the genetic laboratory manipulation of fruit fly body segmentation and appendages. Pretty much puts their CFD causality into the tank.
Posted by: theshortearedowl | July 15, 2009 10:35 AM
Ok, so evo-devo isn't exactly my field, but isn't everyone getting a little excited here? I thought fluid pressure/hydrodynamics if you like were an important part of how cell lines differentiated in a growing embryo.
"Fleury and Pivar must not know about the genetic laboratory manipulation of fruit fly body segmentation and appendages. Pretty much puts their CFD causality into the tank."
They were talking about tetrapods. Insects are much more plastic in body plan.
Posted by: Bernard Bumner
|
July 15, 2009 10:48 AM
Not really; Fluery has published, and now he has a duty to respond properly (or not at all on this forum) to legitimate criticisms. His failure to do so, and instead engage in obfuscatory whining, is rightly a source of irritation.
I'm not sure anyone is actually disagreeing with that.
The problem seems to lie with Fluery's claim that he's found somemthing revolutionary, when he's failed to address any of the direct problems with the manuscript, of his blinkered interpretation of his own sparse data, and the lack of synthesis in his work.
After all, he apparently wrote:
Now, I have no idea what that means, other than that he holds contempt for entire fields of scientific endeavour which seem to everyone else to underlie or better explain the phenomena addressed in his work.
Posted by: theshortearedowl | July 15, 2009 10:58 AM
"the antero-posterior construction of animals is bullshit, the induction of limbs by genes is bullshit..."
Ah. Must have missed that bit. Never mind!
Posted by: Oldcola
|
July 17, 2009 1:27 PM
There is a little bit more about that here:
(emphasis mine)Posted by: vincent fleury | July 29, 2009 11:04 AM
oh, I see the defamatory claims have continued, oh dear.
It is all so simple : people have for long thought that tetrapods were formed by genetic inductions along gradients of morphogenes organized along an antero posterior axis.
This is wrong. Tetrapods are formed by a flow of cells which has a hyperbolic (saddle) point around the navel.
it is not tautological. They form from the navel upwards, and from the navel downwards, with a partial symmetry, quite obvious by the way, once you know it.
Such vortices cannot be interpreted in terms of scalar gradients of chemical concetrations.
Many people, including Mr Myers seem not even to be aware of the fact that there exists vortices in embryos, and they defamate people so easily, so pathetically.
I suppose the day he learns by a colleague that such vortices do exist he will withdraw his comments and apologize.
Posted by: Bernard Bumner
|
July 29, 2009 11:25 AM
Then you need to explain why the genetic data fits the (wrong) theory so well, or at least where such genetic data fits into your own theory.
You cannot simply dismiss pervious theory and data, and especially not in such well-studied areas as this. I believe that all anybody has ever asked you to do is explain yourself - you refused, and said it was not a matter for this kind of forum. Fine then, but don't keep visiting here to tell people how wrong they are, whilst refusing to answer questions and insisting that your conclusions are obviously true.
Posted by: vincent | July 31, 2009 7:24 AM
"Then you need to explain why the genetic data fits the (wrong) theory so well, or at least where such genetic data fits into your own theory."
it is all explained in the paper
Posted by: Oldcola
|
July 31, 2009 11:21 AM
Questions, unanswered in the paper, waiting for your explanations, if there is any, Dr Fleury:
http://tinyurl.com/vfalc1
http://tinyurl.com/vfalc2
Posted by: PZ Myers | July 31, 2009 11:32 AM
Anyone who is familiar with the developmental biology literature would know that lineage tracers have been a popular technique for over a century -- we've been watching cells move (or not move) in embryos for a long, long time.
There are no vortices of cell movement centering around the navel. Period.
Posted by: vincent fleury | August 2, 2009 5:36 PM
Prof. Myers, do not be so peremptory, please, and pay attention to all the data accumulating, you can see these vortices for example at the site of gastrulation.org:
http://www.gastrulation.org/
see the movies movie15.1 and movie15.3
I give a short survey of more recent data at the webpage
http://www.msc.univ-paris-diderot.fr/~vincent/englishEnresume3.htm
these vortices have been known for a century, and observed in better detail in recent years, there importance was completely overlooked.
They have a neutral point, of speed equal to zero in all directions (stagnation point), as evidenced by several authors, duely quoted in my papers and that webpage.
see especially the work of Kees Weijer and colleagues at Dundee University.
I made the connection to the navel in two papers :
1-Vincent Fleury, An elasto-plastic model of avian gastrulation, Organogenesis, 2, 1, 6-16, 2005.
2-Thi-Hanh Nguyen, Anne Eichmann, Ferdinand Lenoble, and Vincent Fleury, Dynamics of vascular branching morphogenesis: The effect of blood and tissue flow, Phys. Rev. E 73, 061907 (2006)
If I could put images here, I would gladly add several spectacular images of such vortices.
These vortices exist at the blastula stage, during early gastrulation "around" the presumptive navel. This is to say, revolving towards and away from the presumptive navel area.
As the embryo folds, the topology of the flow is passed to the body of the animal, even when it no longer revolves, but the topology is fixed by the early pattern of cell paths
These early vortices exist. They do, Mr Myers. I am sorry that this should be so painful to you, and difficult to understand, even to see.
During the revolutions performed by these cells, the body extends and contracts by the laws of physics, and the entire movements become progressively slowier, as the embryo stiffens. However, as the body contracts towards the still presumptive navel, the lateral plates bulge out by conservation laws of physics, and a movement of twist of the tissue can be evidenced, which is a continuation of the early vortices.
Therefore, vortices induce the navel position, and above and below the navel( I mean in the AP direction), four limb fields (2 in the shoulder area, two in the pelvis area) formed by physical forces.
These vortices, by the way, are shown on almost all plates of human embryology, spontaneously, without even mentioning it (see for example the plate with the definition of the placenta, in which the overall revolving bending of the tissue is clearly shown, without even being conscious of it at :http://www.cosmovisions.com/placenta.htm):
It is of course sad for me, and even strange that you should deny that vortices exist, considering all the harm you have already done to me, for so cheap. But the small change you will be given might cost you more if you await too much to open your eyes. It is defamatory to state that these vortices do not exist, and use such a statement to ridicule me publicly.
I am a regular scientist, working at a regular university, a civil servant, and not a crackpot. I am only one of your colleagues, nothing more, nothing less, kindly telling you that you missed something.
You should relax, and take some calm time to have a look at recent data. Please do, it is extremely interesting, and important. Please. Do.
With my best regards, I wish you a happy reading.
Vincent
Posted by: Oldcola
|
August 3, 2009 10:08 AM
Dr Fleury,
Always frustrating to not be able to insert images in the comments section of blogs:
Why don't you just present them in your webpage? You do so for other images but not for the most crucial ones. If you need help with preparing the html pages for your display I'm always willing to help you with this issue.
I'm asking for those spectacular images since august 17, 2007. For the moment you failed to produce them.
One more time: four vortices to be clearly visible, in order to be able to evaluate any possible correlation between their center and the presumptive limbs' field/bud.
Independently of the couple of invisible up to now vortices, L2/R2 which you relate to the hindlimbs, your interpretation of how they would influence limbs flexion, if they existed, seems badly flawed and my questions [#152] remain unanswered; as much as those concerning the FGFs expression regulation by pressure [#61].
It's really quite weird that you carefully avoid direct answers; do you have any other reason to do so than just being unable to provide them?
Posted by: vincent Fleury | August 3, 2009 10:50 AM
Oh dear, this IS internet. Bravo.
Posted by: GilbertNSullivan
|
August 3, 2009 11:39 AM
@Vincent
Oldcola's seems like a reasonable request to me... in fact it's almost as though you're being encouraged to respond and defend your (somewhat idiosyncratic) claims. On your own website. Where you can post many, many pictures of vortices.
Either that or the bar for crusading is awfully low these days...
Posted by: Oldcola
|
August 3, 2009 1:53 PM
@156
That certainly is Internet and the Web in particular, we may be grateful to Tim Berners-Lee for it; I am.And as much certainly, this is not an answer to my questions.
Posted by: Sven DiMilo | August 3, 2009 2:02 PM
You guys know about the new post & thread?
Posted by: ermine | August 3, 2009 8:00 PM
Wow! Angry kook are angry, huh?
Amazing how he avoids direct questions and refutations, whines about how mean everyone is, all the while being even more dismissive of anyone else who has any criticism. Does he think he's the first 'regular scientist at a regular university' that has had his theories torn to shreds on this most excellent blog? Michael Behe is the first example I can think of, but there are certainly others - Like Stuart Pivar! Aannd there he is!
Judging entirely by 'Dr.' Fleury's actions here in this forum, I'd have to label him a crackpot of the first order. He's refused to answer very specific, simple questions, (We KNOW how and why limb buds form, and it's not 'vortices' or 'pressure'! See #69 above.), he's been unable to show any real evidence of these supposed 4 vortices, (See #155), and even as he decries the hurtfulness of the comments, he does exactly the same thing in every post!
He's certainly answered MY questions about the strength of his theories. '[T]he induction of limbs by genes is bullshit,... the selection of tetrapods by evolution is bullshit'? Really? He's got a hell of a lot of work to show before making statements like that, and he hasn't shown it here OR on his web page, that's for sure.
Thank you Dr. Fleury, for removing the doubts I had at the beginning of this thread. You've done a brilliant job of making a fool of yourself.
Posted by: truthspeaker | August 3, 2009 8:04 PM
Mr. Fleury, you can post links to images in comments the same way you would link to a webage.
Posted by: Danny | August 4, 2009 10:47 PM
Dr Fleury, your paper needs to be greatly reduced.
Or perhaps completely oxidized.
Posted by: vf | October 24, 2009 10:57 AM
http://www.msc.univ-paris-diderot.fr/~vincent/monmodele/vortex1.jpg
Posted by: Aratina Cage
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October 24, 2009 11:56 AM
Re: vf #164
Why is it that photos of Sasquatch are always so blurry? I just can't make out the Sasquatch in the photo you provided. The squiggly green lines don't help. Are you trying to trace the hair on the Sasquatch or something?
Posted by: Sven DiMilo | October 24, 2009 12:32 PM
Wow, did Fleury just return to a thread dead for months except for spam (hi, Kat!), only to post a single photo of his putative vortices?
That's just really interesting behavior.
Posted by: David Marjanović, OM | October 24, 2009 5:23 PM
Oh for crying out loud. This (bad) photo shows a chicken embryo that hasn't even finished neurulating. Limb buds start forming much later.
And the green strokes and blue crosses correspond to what in the photo?
Literature, Dr Fleury. Start reading the recent development genetics literature (primary literature since the mid-1990s, textbooks since a bit later). You keep acting like a creationist who has no idea how much knowledge even exists.
Posted by: Sven DiMilo | October 24, 2009 5:28 PM
One assumes they trace the migration routes followed by individual cells (neural crest in this case?). See the vortices? NOW DO YOU SEE 'EM?
Posted by: Nerd of Redhead, OM
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October 24, 2009 5:37 PM
Also unprofessional in not knowing the knowledge that exists to debunk your inane and insane idea.Posted by: David Marjanović, OM | October 24, 2009 7:09 PM
Migration routes? At that stage? The cranial (in the photo: right) border of the area with the green strokes is the cranial border of where the neural canal hasn't closed yet. The neural-crest cells start migrating when the closure happens. Where the green strokes are, it hasn't happened yet.
Still not.
No, I can't find anything obviously crazy about it. It just happens to be wrong – and that just happens to have been known for about 20 years, if not more (transplantation experiments from the early 1980s and earlier...). This is where the deep, deep embarrassment lies.
Posted by: vf | November 1, 2009 11:15 AM
Oh I see some people are never satisfied,
actually, there were other images and also a movie,
I provided just one because I was asked to do so.
The green tracks are tissue tracks starting from the blue crosses, with 5 minutes interval. The Time-lapse lasts 5 hours.
It is a chicken embryo.
Please find more data at:
http://www.msc.univ-paris-diderot.fr/~vincent/
in french and at
http://www.msc.univ-paris-diderot.fr/~vincent/englishvincent.html
in english.
I have other "insane" movies, of course.
Regards
Posted by: Tuff | November 10, 2009 7:45 PM
vf's links ---> page not found.
Posted by: Oldcola
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November 12, 2009 4:47 AM
@Tuff
They are building a somehow differently organized website for the lab (msc).
Hopefully Fleury's stuff will reappear in a near future so we will be able to discuss the discrepancies with his published model.
(my comment must be stuck at the moderation pile, too many links I suppose)
Posted by: vincentfleury
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November 17, 2011 2:45 AM
An end point has been put to this stupid post by Mr Myers and this stupid comment thread, by the publication in series of :
1. Fleury V. A change in boundary conditions induces a discontinuity of tissue flow in chicken embryos and the formation of the cephalic fold. Eur Phys J E Soft Matter. 2011 Jul;34(7):1-13. Epub 2011 Jul 28.
2. Fleury V. Dynamic topology of the cephalochordate to amniote morphological transition: a self-organized system of Russian dolls. C R Biol. 2011 Feb;334(2):91-9. Epub 2011 Jan 7.
3. Fleury V., Boryskina O. P., Al-Kilani A., Hyperbolic symmetry breaking and its role in the establishment of the body plan of vertebrates. C R Biol. 2011 Jul;334(7):505-15. Epub 2011 Jun 22.
4. Boryskina O.P., Al-Kilani A. and Fleury V. (2011). Limb positioning and shear flows in tetrapods. The European Physical Journal Applied Physics, 55, 21101 doi:10.1051/epjap/2011100468
5. Boryskina O.P., Al-Kilani A. and Fleury, Body Plan of Tetrapods, is it patterned by a hyperbolic flow?, Cell Cyle, November 15 issue, 10:22, 1-2 (2011).
Regards
VF
Posted by: Jerry R
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December 19, 2011 1:58 PM
It seems to me that this is a constructive discussion, albeit very aggressive.
I think the biggest problem with Fleury's attempt is that he maps target patterns to a level that's disconnected, that is, the thing that's spiraling is not shaped like a skull.
If he would apply his methods to Weijer's data or others in which the patterns are observed and relates actual components, ie., cells and gene products, who would object? In fact, isn't that the whole point of Goodwin's research? We have the methods, now let's use them!
Posted by: derwood
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January 28, 2012 9:05 PM
"These vortices exist at the blastula stage, during early gastrulation "around" the presumptive navel. "
There is no navel in a chicken blastula. Not even in a chicken gastrula. Not even a presumptive one. There is no navel - even a presumptive one - until well after gastrulation.
Posted by: vincentfleury
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February 19, 2012 4:37 PM
@You are quite wrong, I actually published my first article before Weijer's article
The target pattern sin the skull is a very late thing, most of the work relates with vortices at blastula, gastrula and neurlation stages.
@@Derwood, you don't understand, the blastula revolves and eventually you have a navel at the location of the saddle point. Indeed the final navel as we know it is "well aftergastrualtion", but the chain of causes and effects that leads to it starts witht he existence of a hyperbolic point in the flow.
I do not know why M. Myers is not aware of any of the articles dealing with vortex flows in embryo development (including in flies by the way), except that he is probably not an actual scientist.
I hope we meet together some day, either in Minnesota, or in Europe. If he is a man, he will soon understand how wrong he is.
Posted by: vincentfleury
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February 19, 2012 4:39 PM
@You are quite wrong, I actually published my first article before Weijer's article
The target pattern in the skull is a very late thing, most of the work relates with vortices at blastula, gastrula and neurlation stages.
@@Derwood, you don't understand, the blastula revolves and eventually you have a navel at the location of the saddle point. Indeed the final navel, as we know it, is "well after gastrualtion", but the chain of causes and effects that leads to it starts witht the existence of a hyperbolic point in the flow.
I do not know why M. Myers is not aware of any of the articles dealing with vortex flows in embryo development (including in flies by the way), except that he is probably not an actual scientist.
I hope we meet together some day, either in Minnesota, or in Europe. If he is a man, he will soon understand how wrong he is.
Posted by: 'Tis Himself, OM
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February 19, 2012 6:00 PM
Dr. Fleury,
You're a physicist, Professor Myers is a biologist. If I were to make a bet about who has a better understanding of biology, you would come in second place. Pretending that a PhD biologist is "probably not an actual scientist" because he disagrees with a physicist on a biological question shows you're taking Myers' criticisms much too personally.
Posted by: vincentfleury
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February 20, 2012 1:20 AM
Nope.
I would perfectly well admit that "he disagrees on a biological question", as you say.
The point is that he considers as "non existent" a biological fact, perfectly well admitted now in biology, and ridicules people loudly, instead of just having a look at all this. So he does not even admit the existence of rotatory flows in embryo as a true scientific questions (he still quotes my name constantly with the "kooks" tag). This is not the behaviour of a scientist. A scientist has to be open minded to intellectual surprises.
Posted by: Nerd of Redhead, OM
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February 20, 2012 6:41 AM
Yawn, the unprofessional Fleury is back doing his unprofessional defense of his inane paper. Folks, this is not how one should do science. Once the paper is published, it should be dealt with by other professionals without interference by the author unless specially asked. Which wasn't the case here.
Only cranks and crackpots engage in the long winded inane unprofessional behavior of Fleury. A PRIME EXAMPLE of what not to do.
Posted by: Stanton
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February 20, 2012 8:38 AM
Open-mindedness does not mean "mindlessly agreeing with whatever you say."Posted by: vincentfleury
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February 20, 2012 8:39 AM
I believe it very interesting for the readers of this blog, and especially the young would-be scientists, to analyze how exactly science is "dealt with" here, by PZ Myers, and anonymous characters like yourself.
Every time M. Myers insults me on his blog, and he still does, I will defend myself simply.
I understand this blog is a fascist place, and watch it with curiosity as such.
Posted by: vincentfleury
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February 20, 2012 8:48 AM
@ Stanton : "mindlessly agreeing with whatever you say"
Open your mind and eyes : the ENTIRE scientific community in this field has recognized the existence of vortex flows in embryo development.
Just do "vortex flow vortices embryo development blastula" in google, already four different authors show up in the first page : Chuai et al. Sandersius et al. Vasiev et al. and Myself.
You are approving brutal methods of an ignorant : Prof. Myers.
Posted by: Nerd of Redhead, OM
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February 20, 2012 9:01 AM
As usual, the unprofessional crank and crackpot has it backwards. Fleury is a classic example of not how to behave, and any assistant professor caught doing the same thing here in the US would most likely not get tenure due to unprofessional behavior. First rule of holes Fleury is to stop digging.Fleury doesn't grasp the concept that NOBODY has to agree with him, and he prefers to attempt to bully people who disagree with his crank idea, rather than letting his idea speak for itself, like any true scientist would do. I don't have to agree with him, and won't until a majority of the biologists come around to his way of thinking. I'm not holding my breath.
Posted by: Stanton
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February 20, 2012 9:29 AM
If the "ENTIRE scientific community" agrees about it, then how come only thirty such papers come up in an engine like scholar.google.com ?
Posted by: vincentfleury
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February 20, 2012 9:32 AM
I do not understand your question; the number of papers on a new topic starts by 1 and then rises progressively. Just watch the dates of publication, and please inform M. Myers of your discovery.
Posted by: David Marjanović
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February 20, 2012 10:41 AM
Oh, really? Show me.
What flows, and what drives this flow?
A scientist doesn't propose ideas that were disproved long before they were ever proposed.
...means, you're not a scientist.
Fuck you. There are very good reasons for internet anonymity; I don't have a pseudonym because I'm too lazy to think a good one up.
LOL!
Then why do all textbooks openly contradict it, liar?
That's right: you're a liar. What you're saying is wrong, and you know it.
Posted by: vincentfleury
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February 20, 2012 10:49 AM
Oh, really? Show me :
http://www.msc.univ-paris-diderot.fr/~vfleury/embryoportal0.html
Posted by: David Marjanović
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February 20, 2012 11:13 AM
What? That's a movie of gastrulation. The blastula doesn't rotate, it invaginates itself, as you can clearly see in that movie.
Posted by: vincentfleury
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February 20, 2012 11:19 AM
No. It is a 2D frontal view of the flat chicken blastula, is rotating in-plane. The blastula invaginates only by the very end of the movie, when gastrulation actually starts, along the primitive streak, as you can see in this movie:
http://www.msc.univ-paris-diderot.fr/~vfleury/movies/emb505reg.gif
Posted by: PZ Myers
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February 20, 2012 11:28 AM
Are there tissue movements in development? You betcha.
Are there physical effects, and even specifically vortices? Sure thing, I'll mention the generation of vertebrate left/right asymmetry as a perfect example.
Do these instances justify a vague and sweeping, poorly defined declaration that you have a formula that uses fluid dynamics to explain everything? No.
You're an obsessed kook. If you'd actually read what I wrote up there, you'd notice that I acknowledge the importance of physico-chemical interactions in development...what I find ludicrous is your useless and absurd infatuation with one kind of process as the be-all and end-all of morphogenesis.
You're a crank. A nut. A monomaniacal wacko. You can stop emailing me and reviving these comment threads -- they just confirm your lunatic status.
Posted by: vincentfleury
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February 20, 2012 11:31 AM
Ok so here we are Prof. Myers finally admits that there are vortices? Specifically vortices. Don't you?
It is time to apologize. Poor old chap.
Posted by: apokryltaros
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February 20, 2012 11:37 AM
That is not what he said, and you know it. Yes, yes you should apologize for having wasting everyone's time here trying to bully Professor Myers into swallowing your bullshit.Posted by: PZ Myers
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February 20, 2012 11:45 AM
Are you really that stupid, Fleury? Of course vortices exist: I even wrote about them long before I kicked your lazy paper to the curb, as for instance their role in setting up nodal asymmetries. So?
The issue isn't whether tissues flow in interesting ways in development, it's whether your inane model accurately predicts anything.
Look again at the last 3 paragraphs of this post, where I ask you specific questions and ask for specific support for your wacky assertions. Pointing to isolated examples of fluid flow in embryos DOES NOT support your sweeping hypotheses.
They do support my hypothesis that you are a deranged twit, however.
Posted by: Nerd of Redhead, OM
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February 20, 2012 11:47 AM
No, it's time for you to acknowledge you are a non-scientific crank and nutcase. Your over-the-line obsession with vortices doesn't mean you are right. One case doesn't make you right. You need hundreds, if not thousands of cases, for vortices to mean something in biology. Otherwise all you have is your ego and delusions. Typical egotistical bully and crank.Posted by: Bill Dauphin, avec fromage
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February 20, 2012 12:28 PM
OK,let me admit up front that I realize this is probably just an artifact of unfamiliarity with the usage conventions of a language that is (apparently) not your mother tongue, but this...
...made me laugh. Protip: In future, if you have any hopes of being taken seriously, and of not having people imagine you think of yourself as a deity,do not capitalize myself. Jus' sayin'....
Posted by: vincentfleury
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February 20, 2012 12:39 PM
@PZ Myers
All the possible answers at this stage of research are there in the (several) papers. It just happens that you do not read them, likely because you cannot understand them.
Nodal asymmetries?
Why do you feel like talking about something else?
"The issue isn't whether tissues flow in interesting ways in development, it's whether your inane model accurately predicts anything"
If there are vortices forming the body plan, it is not just "an interesting way" of flow. The model predicts that, in a viscous flow, with a hyperbolic symmetry breaking, an initial flat and round blastula becomes an elongated slender folded sheet, with four bumps along the sides, among other things. By the flow itself, at constant force.
Readers of your final replies will judge by themselves. This work does not deserve your insults and you are a low kind of person.
Posted by: Nerd of Redhead, OM
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February 20, 2012 12:50 PM
We have decided for ourselves. You are a crackpot and egotistical crank, who is thoroughly unprofessional and should be fired by your department head. Nothing you say can be taken seriously until you revert to professional behavior. Which means you quit infesting blogs that gave your inane paper a bad review.Posted by: David Marjanović
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February 20, 2012 12:55 PM
Excuse me, how can it rotate when the top half of the picture rotates to the left and the bottom half of the picture rotates to the right?
The movie, and the other one, show the formation of the primitive streak = blastoporus, the first step of gastrulation.
Then why aren't all gnathostome blastulae flat???
(Because not all are lying on top of a huge yolk, that's why. Every textbook will show you the way most frogs, specifically Xenopus laevis, gastrulates; try to understand how that works, and then try to understand how it works when draped flat over a huge yolk.)
Unfortunately, your "work" deserves every single one of those insults, because you're simply talking about a topic that you don't know hardly anything about.
Posted by: vincentfleury
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February 20, 2012 2:14 PM
Thank your for your first question
there are several vortices with a hyperbolic point
please find PIV trackings of the vector field at this address
http://www.msc.univ-paris-diderot.fr/~vfleury/englishtourbillons2.html
and related pages.
These things have been known for long. I am sorry that you do not know vertebrate embryology (early stages, amniotes)
I can answer other questions but it is late I have a family life.
Best regards
Posted by: Nerd of Redhead, OM
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February 20, 2012 2:55 PM
Yawn, still not convincing me. Try a couple of years from now when science has looked at your paper and either ignores it, or deems it worthy of citing. Until then, be professional: go and stay away.
Posted by: apokryltaros
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February 20, 2012 3:01 PM
Not until we bow down and worship Fleury for his inane, alleged paradigm-sundering paper.Posted by: vincentfleury
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February 20, 2012 3:08 PM
@Then why aren't all gnathostome blastulae flat???
All gnathostomes form from one small part only of the blastula, which is a shell, as we say in physics, it can be round of course, vortices occur also on spherical surfaces (see eddies on ocean surfaces), but the topology of the embryonic problem is that of a flat shell.
Posted by: Nerd of Redhead, OM
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February 20, 2012 3:09 PM
Yawn, funny how trolls (after all, he revived this dead thread which is trollish behavior) like Fleury keep trying to get the last word in, instead of being professional and fading into the bandwidth.
Posted by: vincentfleury
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February 20, 2012 3:10 PM
@Try a couple of years from now when science has looked at your paper and either ignores it, or deems it worthy of citing. Until then, be professional: go and stay away.
Only if until then Prof. Myers stops insulting me and apologizes.
Posted by: 'Tis Himself, OM
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February 20, 2012 3:29 PM
Why should Myers stop insulting you? You're quite obviously an obsessed kook (this is not an insult but a description, one which I can justify). If you want an apology, the here's one: I'm sorry you're an obsessed kook.
Posted by: Bill Dauphin, avec fromage
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February 20, 2012 3:38 PM
Interesting: @200, M. Fleury cannot continue because he has a family life; a mere 54 minutes later (@203), he's back to continue fighting the
goodoblivious fight.Conclusions are left as an exercise for the student.
;^)
Posted by: Nerd of Redhead, OM
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February 20, 2012 3:42 PM
Hmm, lets see. PZ offered real criticism. You can't take any critism due to your overwheening egotism, and you troll his blog because of your crank theory not being accepted without good evidence, and your personal egotism, that is far from realitic on either point.Nope, you need to apologize to PZ for your incessant and irrational trolling, and to the scientific community for your unprofessional behavior. We are waiting...
Posted by: vincentfleury
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February 20, 2012 3:42 PM
Dinner was ready.
Posted by: vincentfleury
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February 20, 2012 3:50 PM
I returned only to answer a specific question. I see that if I do not answer questions, I am insulted. If I do answer questions, I am also insulted.
This place is a fascist one, and fascists ought to be fought.
Posted by: Nerd of Redhead, OM
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February 20, 2012 4:31 PM
The only fascist here is you. You make it all about you. You listen to nobody else, even those who give you good professional advice. You don't need to answer questions, as nobody is truly interested your paper.You should just fade into the bandwidth and cease your unprofessional, fascist, and egotistical behavior here. Look at your future, rather than your past.
Posted by: vincentfleury
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February 20, 2012 4:42 PM
You are not the audience. The audience is the young students of Minnesota or other places who might read this, and who will be clever enough to see who tries to answer questions on interesting new scientific things, and who are the insulting ignorants who insult, defame and scorn, without having the slightest idea of what they are talking about.
Prof. Myers needs ennemies, let him have ennemies.
Posted by: Nerd of Redhead, OM
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February 20, 2012 6:16 PM
And my audience is the same folks, with me showing them that you are an unprofessional crank who should be ignored and scorned for their published drivel, and their overweening egotism in thinking anybody is interested in them for that drivel.Try being professional for a while, and cease trolling here.
Posted by: vincentfleury
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February 22, 2012 7:15 AM
Hi Folks,
this is what "Prof." Myers wrote earlier on :
We've been watching cells move (or not move) in embryos for a long, long time. There are no vortices of cell movement centering around the navel. Period.[...] This is complete nonsense, of course; while cells certainly move in interesting ways, the movement is not sufficient explanation of the phenomena, and it's definitely not true that you can describe development as occurring from the navel outwards.
This what he now writes :
"Are there tissue movements in development? You betcha. Are there physical effects, and even specifically vortices? Sure thing, I'll mention the generation of vertebrate left/right asymmetry as a perfect example"
And here you find the vector field of movement in the presumptive navel area :
http://www.msc.univ-paris-diderot.fr/~vfleury//vortex/vortex1c.jpg
And please F* off, Myers.
Posted by: PZ Myers
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February 22, 2012 7:49 AM
Patently dishonest. Showing that cilia generate vortices that skew the distribution of molecular signals to generate right/left asymmetries is not the same as saying that cells are swirling around the navel. Your desperate attempt to extract vindication for your bonkers ideas from legitimate sources is one of the things that marks you as a kook.
You're writing on my blog. You don't get to tell me to fuck off.
Posted by: vincentfleury
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February 22, 2012 7:55 AM
Just apologize and we can go for a drink together
Posted by: Stanton
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February 22, 2012 8:34 AM
You've been harassing Professor Myers for weeks, demanding that he retract his statement that your paper is wrong and inane, trolling his blog for an apology you do not deserve in this lifetime, you tell him to fuck off because he has yet to be impressed by your inability to get a clue, and now you want to bribe him into apologizing by having a drink together?
You're an asshole on top of being an idiot, vincentfleury.
Posted by: Stanton
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February 22, 2012 8:51 AM
Seriously, vincentfleury, you do not deserve an apology. Ever. I would say "the only apology that is deserved is an apology to PZ Myers from you for having bothered him in the first place," but, it's going to go in one eyeball and out the other.
Seriously, the scientific community is not 4Chan: haunting Professor Myers like the Ghost of Christmas Odors Past in the hopes of wringing an apology out of him will never work. It makes you look unprofessional and unpleasantly childish. Furthermore, if you really are right about your silly embryonic vortex hypothesis, it won't matter what Professor Myers thinks, as you will be vindicated in the textbooks. On the other hand, I find a professor of Biology much more trustworthy about matters of embryological development and Biology than a flaky, trolling physicist with a large chip on his shoulder.
Posted by: Bill Dauphin, avec fromage
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February 22, 2012 9:36 AM
M. Fleury:
I have no standing to criticize your science — and in any case, people whose judgment I trust are already doing an excellent job of that — but I'm as qualified as anyone (and moreso than many) to criticize your writing and modes of discourse.
Scare quotes? Really? Do you doubt that PZ is actually a professor? That much, I'm reasonably sure, is a matter of public record, and the fact that you're having a bit of a snit is insufficient to demote him.
Or perhaps I should adapt your mode of discourse to my first sentence above? Thus...
You can't possibly have any objection to that formulation, right?
Posted by: vincentfleury
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February 22, 2012 10:42 AM
Thanks for these interesting comments.
Frankly I do not know who these anonymous commentors are, I address mostly Myers students and colleagues.
But I do know who Prof. Myers is. He is a professor of biology who has been insulting defaming and ridiculing me for years, constantly, and again recently, this is why I return to fix this. He does so, and continues, although he is completely unaware of recent scientific progress, adn pontifies loudly on things he does not know. Unless he apologizes, he deserves a good spanking on his bottom.
His comments on this work, in previous posts, and which ended in
"Patently dishonest. Showing that cilia generate vortices that skew the distribution of molecular signals to generate right/left asymmetries is not the same as saying that cells are swirling around the navel. Your desperate attempt to extract vindication for your bonkers ideas from legitimate sources is one of the things that marks you as a kook."
are pure and transparent sophisms, for any normally thinking scientist. He can certainly foo freshmen undergraduates, but he knows perfectly well that this statement is aporetic, and inconsistent, and will not fool grown-ups.
Either he acknowledges that there are vortices during the establishment of the body plan, which is new, and he henceforth apologizes.
Or he does not, and then he has to provide experimental data that contradicts what I have been giving for years in published articles.
The constant insults of Prof. Myers, on an interesting scientific question, while he is been given considerable experimental data again and again, and new references by myself and others, just shows that he does not deserve the title of Professor, hence the quotes.
Unless he apologizes.
And I will fraternally have a drink with him.
What is going on in developmental biology is all too interesting.
Posted by: apokryltaros
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February 22, 2012 12:07 PM
Or, more likely, Professor Myers will remove your ability to post on his blog due to your constant trolling and asshole behavior, and let his spam filter deal with your incessant emails.
Posted by: vincentfleury
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February 22, 2012 12:19 PM
He can certainly do it. If he does, let the readers decide what it truly means.
Posted by: apokryltaros
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February 22, 2012 12:32 PM
Prof Myers blocking you would mean that you have finally exhausted his patience with your asshole behavior.I mean, honestly, are you that selfishly dense to think that you're going to be censored for your alleged paradigm-changing idea?
To paraphrase someone, the Internet is not free, and you do not have the right to post as you please: the Internet is a collection of privately owned websites, some of whose owners, managers and caretakers give you the privilege of posting.
If you act like an asshole, these website owners/managers/caretakers are fully within their rights to revoke your posting privileges. And that is not censorship. Unless, of course, you would like to explain why preventing someone, like you, from engaging in trolling and harassment is censorship.
Then again, not that you care. All you care about is bullying and harassing Professor Myers over sour grapes because he won't worship you for your alleged paradigm-changing idea.
Posted by: David Marjanović
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February 22, 2012 2:10 PM
But you didn't answer it. What makes you claim that the blastula rotates?
I've seen a blastula rotate (in a movie). That was right after it grew cilia and right before it hatched and swam off. It went on to grow into a sea urchin, not a vertebrate.
That's flat-out wrong. It's hard to imagine you don't know that most frogs form from the entire blastula, to take just the most obvious example where there isn't a potentially confusing yolk sac.
You're right about marsupial and placental mammals, if you even want to use the term "blastula" for them in the first place. But you're dead wrong about gnathostomes (jaw-bearing vertebrates) as a whole.
Only when there's a yolk sac underneath it. The yolk sac can be empty, as it is in placental and IIRC marsupial mammals, but it has to be there for gastrulation and neurulation to take place in a flat geometry. Take a textbook, look at the ontogeny of Xenopus, and gaze in wonderment. It has yolk, but what little yolk there is is all inside the endoderm cells, all of which end up inside the gut during the 3D, spherical event of gastrulation.
Well, no. The navel is the connection to the yolk sac. You're showing us the blastoporus, which is dorsal, not ventral.
If he apologizes, you'll still be wrong.
Friends don't let friends stay wrong!
*burp*
Go find me in Google Scholar. Are you on the Jussieu campus? So was I for years (affiliated with Paris 6, not 7).
This shows very clearly that you understand so little of biology in general that you don't understand what PZ is talking about.
Posted by: vincentfleury
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February 22, 2012 3:04 PM
Thank you for your questions.
No, I am sorry for you you have to revise your conceptions about all this.
-concerning anamniotes like fish or frog, the stucture of the body is aqcuired over a small fraction of the blastula, most of the blastula gives a flacid part under the animal body axis.
-concerning the blastula, it rotates: for god sake, this is extremely well known it has been known for a century, it is called polonaise movements, it was discovered in 1924 by Wetzel. The movement is 2large vortices+2smaller revolutions in the posterior part. See references here
http://www.msc.univ-paris-diderot.fr/~vfleury/portailtourbillons.html
-"the topology of the embryonic problem is that of a flat shell" yes it is, I am afraid you do not know the meaning of the word topology in maths
-about "You're showing us the blastoporus, which is dorsal, not ventral" no in that photo and related movie, it is the part of the blastula that build ups the body it is not the blastopore, you are wrong. At that stage both ventral and dorsal tissue revolves in the same way, I have both the dorsal and ventral views, it is the same 4 rotations pattern, sorry. The ventral view in time-lape movie with a basis of 1 min. is here :
http://www.msc.univ-paris-diderot.fr/~vfleury/movies/emb196x5p0film2.gif
-This shows that there are misconceptions to jump over, and only a fine time-lapse analysis like the ones I do can settle these questions.
I am a simple scientist doing time lapse imaging of growing embryos, and this work does not deserve being ridiculed and scorned.
Posted by: vincentfleury
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February 22, 2012 3:17 PM
Please find here a PIV tracking of the dorsal and ventral movements at the smae stage :
http://www.msc.univ-paris-diderot.fr/~vfleury/vortex/doublevue.jpg
with regards
and also a later image of well established vortices along the body :
http://www.msc.univ-paris-diderot.fr/~vfleury/vortex/vortex6b.jpg
Mind that it is adynamic phenomenon
Posted by: apokryltaros
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February 22, 2012 3:25 PM
Correction: this shows that vincentfleury does not care to understand biology in general. He dismisses Professor Myers' objections as "transparent sophisms" because they are not hyper-saccharine praise.Posted by: 'Tis Himself, OM
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February 22, 2012 4:34 PM
Given a choice between a PhD biologist whose specialty is embryology and a physicist, I know which one is more likely to be right on a question of embryo development.
Posted by: dmcclean.myopenid.com
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February 22, 2012 5:28 PM
Why do these supposed laws of form only apply to vertebrates? Insects, cnidaria, and rotifers seem to me to be sufficiently distinct morphologically to suggest the non-existence of universal laws of the form of organisms. (By universal I mean not-contingent-on-the-evolutionary-history-of-the-species.)
It seems that he started from humans, went up the ladder of classifications until he found the largest one where forms share some consistency, and stopped there for no apparent reason.
Posted by: Stanton
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February 22, 2012 7:45 PM
According to Vincet Fleury, Professor Myers' credentials are magically, automatically forfeit for not mindlessly agreeing with him, though, I do not know how Fleury intends to take way Professor Myers' credentials.Maybe Vincent thinks he can contact the Science Police, and hope he gets a crooked cop to do the deed?
Posted by: vincentfleury
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February 23, 2012 1:15 AM
@thank you for this question.
I work on vertebrates
if you see the development of arthropods you will notice that the gastrulation process and germ band extension correspond to similar vortices revolving in the opposite direction. The consequence is that the early body folds of arthropds are perpendicular to the body axis instead of parallel
in the case of cnidaria, the initial pattern is radial instead of hyperbolic
the origin of these topological differences lie in the structure of the first cleavages of te egg
There are ways to discuss these things without insults
Posted by: vincentfleury
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February 23, 2012 1:22 AM
sorry read @229
Posted by: vincentfleury
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February 23, 2012 2:03 AM
@Maybe Vincent thinks he can contact the Science Police, and hope he gets a crooked cop to do the deed?
Gi'me a break, the biolo-cop is Myers.
Posted by: Stanton
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February 23, 2012 8:38 AM
So says the guy who is harassing Professor Myers, and invalidating Professor Myers' credentials simply because he won't mindlessly agree.Posted by: David Marjanović
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February 23, 2012 9:13 AM
That's correct for most fishes, where the "flaccid part" is the yolk sac, but incorrect for most frogs.
For crying out loud, Google finds 987,000 hits for xenopus gastrulation. Here's one of them! In most frogs, the entire blastula transforms into the tadpole, there is no yolk sac and no extraembryonic membranes.
Why do you keep using this word when it's so inappropiate? The blastula invaginates. Half of the outside goes in. The blastula as a whole doesn't spin around an axis!
You misunderstood me. The primitive streak is the stretched blastoporus, and yes, it is dorsal. The posterior neuroporus later closes over it.
It does, because you're reinventing the square wheel.
Posted by: vincentfleury
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February 23, 2012 9:54 AM
Thanks for your questions and comments;
Ok, you seem to agree that fish and amniotes build up the body plan from a small fraction of the blastula. Please do a little effort forward and have a look at amphibian embryos here
https://www.llnl.gov/str/April05/Loots.html
the body plan is also built up from a small portion of the blastula. The rest is a large pouch which progressively is absorbed into the belly (no contribution to morphogenetic moevements)
In the picture which I believe you were quoting :
http://www.msc.univ-paris-diderot.fr/~vfleury/movies/emb196x5p0film2.gif
The four revolutions occur on the tissue anterior to the primtive streak. The gastrulation has already occured.
These things are subtle. It seems to me you never actually saw a chicken blastula rotation before these posts and my movies on the website.
The blastula, and next the entire surface of the presumptive embryo rotate. They do not rotate around a single axis. There exist four revolutions, around a fixed point. This is called a quadrupolar flow in physics. The fixed point migrates from the anla rea to the umbilical area due to flow dynamics. It is eventually the location of the navel, indeed on the ventral face. But actually the navel is lateral at early stages, and even dorsal : the dorsal aortas follow the path of the stream lines of the vector field, and make a right turn at the position of the hyperbolic point in the center of the flow. This is why the navel is there. The actual navel forms by closure of the gut pocket around the aortas (omphalomesenteric arteries)
It is perfectly appropriate to speak of rotation. There are vortices either complete loops forming entire revolutioning domains, or only partial vortices when the stream line escape the domain. If you do not undertsand what I mean, it is just because you were unaware of these facts. Hence, you should study these questions in more depth, as Myers should do, acknowledge that you have just learned something, that this is not crackpottery; and that's it. We can discuss these things without insults.
The word rotation is perfectly appropriate. Many people, not just myself use the words "rotatory movements", "vortices", " vortex dipoles" etc. I gave you references, you can still do google etc. If you want more just ask, and I give them to youl.
These things were first discussed in 2005.
Posted by: vincentfleury
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February 23, 2012 10:11 AM
sorry I mleant this figure
http://www.msc.univ-paris-diderot.fr/~vfleury//vortex/vortex1c.jpg
Posted by: Nerd of Redhead, OM
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February 23, 2012 10:23 AM
I see Fleury is still engaging in internet stalking, crass egotism, and utterly unprofessional behavior. Fleury, once a paper is published it is up to others to judge it by their professional criteria to see if they find it useful or predictive. PZ didn't find it so by his criteria. He doesn't have to use yours, which is the height of crankism, egotism, and unprofessionalism.
Do yourself a favor and let this go. It is a trivial incident that you, not PZ, keeps turning into a major incident. Understand rule one of science: Nobody has to agree with you. Deal with that elsewhere, preferably with a therapist.
Posted by: vincentfleury
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February 23, 2012 10:24 AM
@David Marjanović
May I kindly ask you : did you actually know that there are rotatory movements on chicken blastula? And that such movements continue at later stages?
Did you happen to learn this because somebody, defending himself against insults and mockery by the celebrated Prof. Myers, has driven you to have a closer look at this question?
Posted by: PZ Myers
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February 23, 2012 10:29 AM
I think it's great that he's doing this. Every time he comments here, it elevates the link to the recent comments list on the main page, and keeps it alive in the google rankings.
Shooting himself in the foot, he is.
Posted by: vincentfleury
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February 23, 2012 10:40 AM
Don't worry, this blog and post is quoted (as rubbish) in published articles, and will be alive for ever.
Posted by: 'Tis Himself, OM
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February 23, 2012 11:25 AM
Fleury,
If your paper is so neato-spiffy-keen, then why doesn't anyone cite it?
Posted by: vincentfleury
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February 23, 2012 11:29 AM
It was cited by Weijer, and a few others actually. But what kind of an argument is this anyway? I show you data, like this :
http://www.msc.univ-paris-diderot.fr/~vfleury//vortex/vortex1c.jpg
http://www.msc.univ-paris-diderot.fr/~vfleury/vortex/vortex6b.jpg
don't you see a pattern of rotation?
So why wave the bat around in air?
Posted by: apokryltaros
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February 23, 2012 11:49 AM
Because you talk and act like an assholeish pinata filled with ego and hot air.Posted by: Nerd of Redhead, OM
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February 23, 2012 4:30 PM
Blog posts aren't quoted in journal articles, as you would know if you weren't a egotistical internet stalker. By the way, those words show both a lack of perspective, and the inability to live with your mistake of that paper. Your problem, not PZ's which should be taken up with a good therapist.After all, this would die down and the thread forgotten the day after you cease your egotistical and paranoid stalking. Your choice, but like PZ says, you are the one looking unprofessional, not him. Now, if your Chancellor, Bursur, (or whatever your VP Acacdemic Affairs is called) sees your egotistical and unprofessional spewing here...think about that.