Oops 090630

vincent fleury:

By the way “I can has L2/R2″ is not a sentence

Aha! this is not a sentence. I was waiting for this one since I read the paper.

For Dr Fleury first step here, and second one here, both necessary to get the flavor.

For everybody else, a puzzle served below [p22 col2 §1]:

The significance of the reversed flexion of the hindlimb in 10% of the experiments reported in reference [59] is unclear since the electroporation experiment used to insert Tbx5 in the hindplate prior to hindlimb growth has a polarity in itself. If this experiment would be confirmed, it would be an uncommon case of a chirality, directly induced by a scalar non-chiral field. This would suggest that Tbx5 codes for a chiral molecule.

Maybe Dr Fleury will take the time to provide the solution. Hopefully this will not end as “I can has chirality??“.

While he is visiting lolcats and fails to have an insight about lolchickens I’ll give it a try to prepare a question for him.


Oops 090619#2

[p21, col 1, §2

Hindlimbs form first during development of most tetrapods, and they are likely to be last to disappear, as known in snakes. The fact that hindlimbs form first and are thus often larger, may be ascribed to the narrow spacing in the caudal part of the early embryo (more below).

Ahem, hindlimbs of most tetrapods form first? Are often larger?

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Oops 090611

Another reference mismatch here:

This dorso-ventral polarity is also present in the hands, with an obvious palmar and a dorsal side. Bio-chemically, this difference seems to be related to the genetic pathway of en1 and wnt-7a [62], and analogous genes may be at play in the dorso-ventral polarity of insect wings [33]. But the expression of specific genetic pathways is related actually to the geometry of the limb bud at the moment of formation: if the limb bud forms from endoderm and ectoderm, it has dorso-ventral polarity (like a normal hand), if a limb bud forms more proximally by a fold of ectoderm only, the limb paddle has double dorsal polarity1 [62].

where ref 62 is

given as E. McGlinn, C.J. Tabin, Curr. Opin. Gen. Devel. 16, 426 (2006), corresponding to: Edwina McGlinn, Clifford J. Tabin, Mechanistic insight into how Shh patterns the vertebrate limb, Current Opinion in Genetics & Development, Volume 16, Issue 4, Pattern formation and developmental mechanisms, August 2006, Pages 426-432, ISSN 0959-437X, DOI: 10.1016/j.gde.2006.06.013.

Which have no mention of en1 and wnt-7a, and doesn’t discuss dorso-venrtal patterning and double dorsal polarity; but it’s written by people understanding limb patterning and AER formation, a nice reading, so you will enjoy it if you are interested by the subject.

But not if you are just seeking information about how Fleury formed his point of view.

On the other forelimb, there is a lot of papers dealing with the dorsoventral patterning of limbs.

We have here a second instance of Fleury’s point of view on how the AER is formed 😀 ROFL etc.

3 The genetics of vertebrate development

In the third section of the paper Fleury starts to display his incredulity of genetic explanations of developmental morphogenesis, concluding by p16, col2, §2:

The review presented here highlights that inductive cascades of unidirectional gradients of scalar quantities cannot explain morphogenesis.

The review is incomplete and often bogus,which explain why Fleury is reaching this conclusion.

Certainly a lot is to be discovered in the field of developmental biology, but also a lot is known and one can’t just ignore it just because it doesn’t fit his point of view.

For those unfamiliar with biology I will try to point gross errors (factual or conceptual) and propose more appropriate readings.

The rhetoric of Fleury’s argumentation will be discussed as well, as they are one of the most interesting elements of the paper and may help understanding his point of view more clearly than his knowledge of the subject.

An overview of what will be discussed.

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Quite clear

This is an excerpt from Flery’s paper, p16, column 1.

However, Popperl et al.’s article deals mostly with the role of lazarus in the cranial (hindbrain and anterior trunk) compartment, (especially it shows how pbx genes participate in the regulatory loop of hox genes needed to specify rhombomere boundaries in the hindbrain) and when coming to limbs gives the same evidence that Tbx5 triggers forelimb outgrowth, since lzr-/- zebrafish do not show fin rudiments at all, and no Tbx5 staining. There is no rationale about limb positioning, apart from a correlation between absence of lazarus, and absence of fins. Especially, it is quite clear that the fin rudiments appear as round balls on the side of the flanks (Fig. 6. I in Ref. [80]). No mechanistic explanation is given of how a collinear series of genes along the neural crest might induce lateral formation of roundish masses of cells (the fin precursor). Popperl’s et al. article deals with deletion of hoxb-5 and hoxb-6 genes, and shows only a very modest shift of the shoulder girdle of about one or at most two vertebrae, when hoxb-5 genes are deleted and no mechanistic explanation. It is difficult to understand from this work in what respect hoxb-5 might be related to limb “positioning”, since when totally absent, there is a normal limb, which is “positioned” by something, and the position is almost normal, except that it is slightly shifted from the wild type.

It discuss material from “Lazarus Is a Novel pbx Gene that Globally Mediates hox Gene Function in Zebrafish”, a paper authored by Heike Pöpperl, Holly Rikhof, Heather Cheng, Pascal Haffter, Charles B. Kimmel and Cecilia B. Moens, and published in Molecular Cell, Volume 6, Issue 2, August 2000, Pages 255-267, doi:10.1016/S1097-2765(00)00027-7.

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I was wrong

Well, I was dead wrong in fact, when a few weeks ago I was writing:

What embryology textbooks our physicist have consulted that doesn’t give the origin of the mesoderm and the subdivisions of the mesodermal plate to paraxial, intermediary and lateral? He should give us the name(s) of the book(s) to avoid it(them).

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The invertebrate morphogenesis

The invertebrate morphogenesis

The second section of Fleury’s paper is about The invertebrate morphogenesis and the example chosen is Drosophila the fly, which is the most studied of the invertebrates but far from describing the “invertabrates” morphogenesis in general, just take a look at a sponge. Two subsections, The fly bauplan and The homeobox genes.

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