4 The paleontological point of view

There is not as much paleontology as one would expect by the title of the chapter. Mostly paleontology is an excuse to further discuss developmental biology, except for subsection 4.1

4.1 Tetrapod origin

If we turn to paleontology, we find a description of tetrapods appearance into three main steps. Appearance of chordates, segmentation of lateral fins, appearance of tetrapods.

That’s the shortest version one can get except “pouf they appeared”. Interesting nevertheless the second step, the “segmentation of lateral fins“. This is one of three hypothetical, not exclusive, working models. Not to be used as a granted fact (see below).

Good news, bad news.

Good news are that Fleury abandonned the idea it appeared in one of his conferences announcement, and promoted in fora, that the tetrapods may have appeared suddenly, with all there attributes, specifying suddenly as “in a single generation“.

But he still think that:

These early tetrapods have well formed complex limbs apparently almost “right away”.

Almost right away being an estimate of the time-lapse between Haikouichthys ercaicunensis, presenting a single median fin-fold and tail, to the tetrapodomorph Tiktaalik roseae; almost right-away corresponds to 100 millions years. At least we are not anymore at the “single generation“level.

Progressive modifications are problematic for a model which is based on a suddenly appearing bauplan.


4.2 About pentadactily

Well, certainly the bests Oops of this subsection. You can read about it here.

The idea to connect somites to fingers was not bad, but it doesn’t stand scrutiny, unless it’s Fleury who compares whatever to whatever (mixing mutants) forgetting or not caring to check the controls, and finally draws false conclusions.

This is not anymore about ignorance but rather about lousy methodology, not particularly connected to biology or physics. Of the general kind.

Reality check says that limb buds facing the same number of somites develop to pentadactylous limbs in wt embryos and nonadactylous embryos to double mutants.

The idea was interesting, but it doesn’t fit reality, so down the drain it goes (an old idea when it comes to Fleury’s theories).

And we find here also one of Fleury’s exact calculations, the “possible period doubling“, with 2*5={8,9,10}, a new kind of arithmetics.

And a second major Oops in the same subsection with the misrepresentation of fig. 21, wrong reference, wrong description.

Fleury wrote a few time ago [source: #63]:

To answer your comment [#50], 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 wonder what that does mean. Because the expected audience was physicists that means that Fleury can serve them BS because they will not understand what they are served? And an embryologist’s opinion make little sense?
He is certainly right to think so, the referees didn’t understood what they were served after all. That doesn’t mean nobody will understand and explain them.


4.3 Fold extension

All fin-like appendages, be it anal, pelvic, pectoral or dorsal seem to be progressive extensions of superficial folds.

Not. Not folds, morphogenic fields (in the embryologist’s sense) which produce buds. There is probably shear stress acting as a positional cue integrated with other ones and participating in the morphogenetic events. But what specifies the morphogenetic field and produce the buds is cellular differentiation, that is differential genetic expression; that’s how folds are produced and what determines where and when they will be produced during the developmental process.

The AER is a typical example of an anatomic structure not being a fold, but an outgrowth of differentiated cells. But then Fleury may consider it as a fold, falsely believing (from a patently ignorant point of view) that in the normal case the AER is the junction of ectoderm and endoderm.

The discussion about the chorio-amniotic fold of the amniotes is interesting. Nothing to do with paleontology, no references concerning the timeline of its development to help connect the embryos curling with the fold‘s formation, an hypothesis out of thin air, expressed as an assertion (“The chorio-amniotic fold is analogous to a fin fold, except that the topology of the edge is a circle which closes up progressively like an iris, to form a hollow bag, and not a flat veil.“).
At least when it comes to the genetic components specifying its development he express his opinion as a belief (“I believe that a genetic analysis of the amniotic edge would give similar genetic inductions as a tail (see data base GEISHA [97]“). It could be, did he checked out the available data that could support this hypothesis? Or does he cite GEISHA just to bring false credibility to the hypothesis?

No mention of the neural fold, in plain sight (fig. 18), which doesn’t fit with the idea of proximo-distally extension.

Charles Darwin is wrongly cited here too. Maybe “scaffold” sounds better in Fleury’s ears, but it wasn’t used by Darwin.

This is also true of other edge-like organs, such as ears, nostrils or lips, which are well known to be observed in nature with almost “arbitrary” lengths, a word often used by Darwin.

Not very often, and never in association with “lenght”.

Citing Darwin doesn’t validate hypotheses, citing him (or anybody else) inappropriately, disrupts the argument.

So,

In the case of the pectoral and pelvic fins, they are believed to originate from a uniform fin present along the body; in the centre of this fin, an area was interrupted or somehow inhibited.

Again, no reference.

There is a quite interesting and relevant to the specific question paper (and for further discussion), by Yonei-Tamura et al.1, addressing the presence of competent stripes for diverse positions of limbs/fins in gnathostome embryos, presenting three, non exclusive, work models:

stripes-of-competence.jpg

Fig. 5. Model for the diversification of appendage morphology and its position in gnathostomes. Top: basic body plan for appendage formation with distinct features as a conserved developmental program; light blue indicates the lateral and dorsal competence for formation of limb/fin buds. Middle: appendages in early gnathostomes are formed by species-specific selection of limb/fin positions from the entire general competent region. Bottom: basic morphology and diversification of appendages in extant gnathostomes had evolutionally been established under the competence. Note that the animal retains competence in the dorsal and flank regions as shown in light orange.

One of them, middle/left of fig.5, fits with the hypothesis favored by Fleury. The authors compared msx1 expression in dogfish, skate and chicken, supporting the model by restricted gene expression domains between the three kinds of embryos (from fig. 2, panel Q1 :

msx1_dogfish_skate_chicken.gif

Schematic representation of msx1 expression in dogfish, skate, and chick embryos. Light and dark orange bars represent msx1 expression in the mesenchyme and ectoderm, respectively.

The skate embryo expressing msx1 in a way that gives an “8-shape” when observed from a dorsal or ventral point of view.

A very interesting information one can draw from this paper is that competence for limbs/fins is conserved to actual gnathostomes’ embryos and it comes in stripes rather then buds restricted at the limbs/fins morphogenic fields. And this information gathered by experimental data, confirming previous observations (including ref [65]).

Thus, the assertion

This is to say that it is not the regulatory loops of the genetic expressions which actually induced the splitting of the fin into limbs, but some “contraction”, which remains to be understood.

was obsolete before cteappv’s acceptation by EPJAP, the contraction being the one of of the limbs/fins morphogenic fields specifying genetic expression. One could have anticipated that this would be the case, from data available through the relevant scientific literature, Yonei-Tamura et al. paper being a systematic confirmation of previous results (which was necessary and is welcome), more than a revolutionary inout.

4.4 Limb extension

The fourth subsection starts quite badly.

Therefore, the situation in this field is not quite clear. It seems again that the same genes, already present prior to limb appearance, may serve to make a tail, a fin, or a limb, depending on where they are expressed, i.e., depending on the local geometrical context, and physical twists which occurred before genetic expression, in addition to chemical differences. This reminds of the fact that cnidarians and vertebrates have similar gene regulatory networks.

Hox genes where co-opted for specification of limbs, the central nervous system, the vertebral column, the gut, the genitals, the excretory apparatus and the hematopoietic system. They produce DNA binding proteins which act either as activators or repressors of transcription, depending of the differentiation state of the concerned cells and the integration of signaling events.
They indirectly (via the genes which expression they regulate) define geometrical context and in turn may be influenced by it as it specifies positional cues. Their role is evidenced by loss and gain of function experiments, limited by the pleiotropy of action of these genes (mutants development may be arrested before the onset to the developmental stage to be studied, e.g. limb development).

For the higher-then-the-cell level, genetic expression always precede geometrical variations, providing the molecular effectors and the energy necessary to produce them. Abrogating transcription (for tetrapods also mRNA maturation) and/or translation (i.e. gene expression) inevitably results in cell death; the single resulting mechanical effect observed being the cell’s collapse and desegregation.

That’s basic biology textbook knowledge and it’s really weird to have to introduce these basic notions while reviewing an already published paper. And they directly contradict the notion of geometrical context and pysical twists occurring before genetic expression.

And facts concerning the similarity of GRNs between cnidarians and vertebrates should be adequately revised.

Later during evolution limbs disappeared from some tetrapod lineages which became aped, such as snakes.

Adult tetrapods may be limb-less because limbs don’t develop. The natural pattern of tetrapods is just tetrapod. If some species doesn’t conform with it’s just not a tetrapod. Easy to grasp, even for physicists. The adult of some species are limbless.
Fleury rightly concludes that for a species to be considered as tetrapod it must be a tetrapod! Puzzling, right?

The fact that hindlimbs form first [...]

is just one (more?) of the authors fantasies and certainly not a general fact, the forelimb-hindlimb developmental timing changes across tetrapod phylogeny. BIBO rule applies here, also.

4.5 Limb flexion

Articulations of the zygo- to auto-pode and stylo- to zygo-pode have being demonstrated to be sensible in respect to their orientation to ectopic gene expression which is able to change them.

This is a huge problem for the model Fleury propose, and his effort to minimize experimental results is ridiculous, and some ensuing statements are quite curious:

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.

If one needed an additional proof that the author really don’t understand what he is talking about, he got it. I really don’t find what to say about the degree of ignorance showcased here, except once more suggest that Fleury should RTFM and avoid talking about transcriptions factors before doing so.

Concerning limb flexion and Fleury’s model:

  1. Limbs grow in a reverse way than the model predicts,
  2. but this isn’t really important as the limbs flexion is represented by the model falsely, the third dimension lacking, and no mechanism is proposed for the instruction of the direction of flexion of the limbs, between the assumed vortices and the orthogonally growing limb.

This is the second predicted feature of the model, after limb positioning and is patently flawed.

Last in this subsection, one more display of Fleury’s poor understanding of biological literature, the way he reports the work of Liao & Collins, unable to make the distinction between an intoxication (reality) and a mutation (Fleury’s point of view) and correctly report on the “duplication of the entire body axis” which the authors report as lethal beyond gestation day 9 (reality) and are here considered necessary for the apparition of additional limbs (Fleury’s point of view).

1. Competent stripes for diverse positions of limbs/fins in gnathostome embryos, Sayuri Yonei-Tamura, Gembu Abe, Yoshio Tanaka, Hiromasa Anno, Miyuki Noro, Hiroyuki Ide, Hideaki Aono, Ritsu Kuraishi, Noriko Osumi, Shigeru Kuratani, and Koji Tamura, Evolution & Development 10:6, 737–745 (2008)

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