Posted: Aug 24, 2018 1:12 am
by Calilasseia
Wortfish wrote:
Rachel Bronwyn wrote:If you study even a single semester of comparative vert anatomy, you're overwhelmed by the similarities between birds and reptiles. They're the same.

Calilasseia wrote:
What evolutionary biologists (which is the proper term for the people who spend decades studying the subject) actually postulate here, is that the same processes resulting in changes that don't involve the formation of new taxa, are also involved in changes that do produce new taxa.

That's really well put.

Birds have feathers, reptiles have scales.

The literature on feather evolution is extensive. This literature includes documentation of discoveries of feathered non-Avialan Theropod dinosaurs. A sample paper is this one:

A Feathered Dinosaur Tail With Primitive Plumage Trapped In Mid-Cretaceous Amber by Lida Xing, Ryan C. McKellar, Xing Xu, Gang Li, Ming Bai, W. Scott Persons IV, Tetsuto Miyashita, Michael J. Benton, Jianping Zhang, Alexander P. Wolfe, Qiru Yi, Kuowei Tseng, Hao Ran and Philip J. Currie, Current Biology, 26: 1-9 (19th December 2016) [Full paper downloadable from here]

Xing et al, 2016 wrote:SUMMARY

In the two decades since the discovery of feathered dinosaurs [1–3], the range of plumage known from non-avialan theropods has expanded significantly, confirming several features predicted by developmentally informed models of feather evolution [4–10]. However, three-dimensional feather morphology and evolutionary patterns remain difficult to interpret, due to compression in sedimentary rocks [9, 11]. Recent discoveries in Cretaceous amber from Canada, France, Japan, Lebanon, Myanmar, and the United States [12–18] reveal much finer levels of structural detail, but taxonomic placement is uncertain because plumage is rarely associated with identifiable skeletal material [14]. Here we describe the feathered tail of a non-avialan theropod preserved in mid-Cretaceous (~99 Ma) amber from Kachin State, Myanmar [17], with plumage structure that directly informs the evolutionary developmental pathway of feathers. This specimen provides an opportunity to document pristine feathers in direct association with a putative juvenile coelurosaur, preserving fine morphological details, including the spatial arrangement of follicles and feathers on the body, and micrometer-scale features of the plumage. Many feathers exhibit a short, slender rachis with alternating barbs and a uniform series of contiguous barbules, supporting the developmental hypothesis that barbs already possessed barbules when they fused to form the rachis [19]. Beneath the feathers, carbonized soft tissues offer a glimpse of preservational potential and history for the inclusion; abundant Fe2+ suggests that vestiges of primary hemoglobin and ferritin remain trapped within the tail. The new finding highlights the unique preservation potential of amber for understanding the morphology and evolution of coelurosaurian integumentary structures.

Later on, the paper has this:

Xing et al, 2016 wrote:DIP-V-15103 is interpreted as a non-avialan coelurosaur tail: its vertebral profiles and estimated length rule out avebrevicaudan birds, oviraptorosaurs, and scansoriopterygians—lineages generally characterized by a short caudal series with subequal centra [25–27], with the exception of Epidendrosaurus. The branched feathers have a weak pennaceous arrangement of barbs consistent with non-avialan coelurosaurs, particularly paravians. Although the feathers are somewhat pennaceous, none of the observed osteological features preclude a compsognathid [28] affinity. The presence of pennaceous feathers in pairs down the length of the tail may point toward a source within Pennaraptora [9], placing a lower limit on the specimen’s phylogenetic position. However, the distribution and shape of the feathers only strongly supports placement crownward of basal coelurosaurs, such as tyrannosaurids and compsognathids. In terms of an upper limit, the specimen can be confidently excluded from Pygostylia; in addition, it can likely be excluded from the long-tailed birds, based on pronounced ventral grooves on the vertebral centra. Additional taxonomic assessment details are provided in the Supplemental Information.

Indeeed, a number of non-Avialan Theropods have now been found with feathers, including Scansoriopteryx, and the Tyrannosaurid Yutyrannus, the latter being a 9 metre long ground based predator. Oh wait, what did I just announce? Oh that's right, a 9 metre long Tyrannosaur with a manifestly feathered integument has been found. the paper documenting this find is this one:

A Gigantic Feathered Dinosaur From The Lower Cretaceous Of China by Xing Xu, Kebai Wang, Ke Zhang, Qingyu Ma, Lida Xing, Corwin Sullivan, Dongyu Hu, Shuqing Cheng & Shuo Wang, Nature, 484: 92-95 (5th April 2012) [Full paper downloadable from here]

Xu et al, 2012 wrote:Numerous feathered dinosaur specimens have recently been recovered from the Middle–Upper Jurassic and Lower Cretaceous deposits of northeastern China, but most of them represent small animals1. Here we report the discovery of a gigantic new basal tyrannosauroid, Yutyrannus huali gen. et sp. nov., based on three nearly complete skeletons representing two distinct ontogenetic stages from the Lower Cretaceous Yixian Formation of Liaoning Province, China. Y. huali shares some features, particularly of the cranium,with derived tyrannosauroids2,3, but is similar to other basal tyrannosauroids4–12 in possessing a three-fingered manus and a typical theropod pes. Morphometric analysis suggests that Y. huali differed from tyrannosaurids in its growth strategy13,14. Most significantly, Y. huali bears long filamentous feathers, thus providing direct evidence for the presence of extensively feathered gigantic dinosaurs and offering new insights into early feather evolution.

The modern molecular biological perspective is provided by papers such as this one:

Evo-Devo Of Feathers And Scales: Building Complex Epithelial Appendages by Cheng-Ming Chuong, Rajas Chodankar, Randall B Widelitz and Ting-Xin Jiang, Current Opinion in Genetics and Development, 10: 449-456 (2000) [Full paper downloadable from here]

Chuong et al, 2000 wrote:Introduction

The vertebrate body is covered by either scales, feathers or fur to provide warmth and protection. Comparing and contrasting the formation of these different integument appendages may provide insights into their common embryonic origin as well as evolutionary divergence. The reptile integument is mainly made of scales [1]. In birds, there are two major integument appendages: scales on the foot and feathers on most of the rest of the body [2••]. Scales provide protection and prevent water loss. The major innovation of the avian integument was the evolution of feathers, which provide novel functions such as insulation, display (communication), and flight. Chickens have three major types of scales, which are morphologically similar to reptile scales (Figure 1a,b [1,3]). Reticulate scales are found on the foot pad: they are radially symmetric and express α-keratin only. Scutate scales are large and rectangular and are the major type found on the anterior meta-tarsal shank and dorsal part of the toes. Scutella scales are distributed lateral to the scutate scales and are smaller in size but are also rectangular. Both scutate and scutella scales have anterior–posterior polarity, with an outer surface composed of β-keratin and an inner surface and a hinge region composed of α-keratin. Cell proliferation is distributed diffusely in scales [4•] without a localized growth zone (e.g. hair matrix or feather collar), dermal papillae, or follicular structures. Feathers are arranged in specific tracts over the body which are divided by apteric zones (regions without feathers [2••]). The base of each feather follicle contains protected tissues, permitting the epithelial–mesenchymal interactions (epidermal collar and dermal papillae) that provide a source for continuous feather elongation and molting. Epithelial and dermal sheaths lie along the exterior part of the feather, whereas pulp is found within the epithelial cylinder during development. A typical feather is composed of a rachis (primary shaft), barbs (secondary branches), and barbules (tertiary branches; Figure 1c). The variation in feather size, shape and texture is complex. With regard to size, feathers of the same bird are of different length and diameter, and often distributed in a gradient. For shape, types range from down feathers that are mainly radially symmetric (the rachis is either absent or very short) and contour feathers the symmetry of which is mainly bilateral. Flight feathers are bilaterally asymmetric (Figure 1c). For texture, feathers can either be fluffy or form a firm vane. The barbules can be bilaterally symmetric to each other and therefore fluffy (plumulaceous), or the distal barbule can form a hooklet enabling it to interweave with the proximal barbule of the next barb in a ‘velcro-like’ mechanism (pennaceous). The calamus is the region of a shaft without barbs. A feather can have different ratios of these structures, thus providing an enormous number of permutations of structural and functional variations [2••,5].

The feather is the most complex vertebrate integument appendage ever evolved. How is a flat piece of epidermis transformed into a three level branched structure? Here we present ten complexity levels of integument appendages that correspond to developmental stages of chicken skin and feather precursors recently identified in dinosaur/primitive bird fossils. Cellular and molecular events that convert one complexity level to the next are discussed, including those converting avian foot scales to feathers.

Page 451 of that paper has a table featuring the genes known to be implicated in different developmental processes, where known.

An interesting part of that paper is this (emphases in blue mine):

Chuong et al, 2000 wrote:Can scales be converted to feathers?

To explore the roles of the epidermis and dermis in appendage morphogenesis, skins from different sources were surgically separated into epidermis and dermis and then recombined for culture. Heterotopic recombinations between midventral apteric and dorsal feathered skin showed that either the presence or absence of feathers is dependent on the dermis [6••,7•]. Heterotopic recombination between feather and scale skin regions showed the same principle. The timing of target tissue competence, however, is another factor to consider. When epithelia of later stages were used, they were more committed and the possible resultant phenotype became more restricted. When leg dermis was recombined with wing epidermis, we expect to see scales form. However, feathers are frequently seen [6••] and this could be explained by the fact that the wing epidermis used is already committed to form feathers when the experiments were performed. Similarly, mesenchymal dental papilla can induce teeth from epidermis during the embryonic stage. However, the recombination between adult rat ear epidermis and dental papilla gave rise to the growth of an enlarged hair [39••]. This is because the embryonic epidermis is truly pluripotential and can form different kinds of epithelial appendages, whereas the potential of adult ear epidermis is restricted and it can only form the hair epithelial appendage. In heterospecific recombinations, the epidermis can respond to dermal messages, which appear to cross species without a problem, but can only make epithelial appendages permitted by its genetic code. Thus recombinants of lizard epidermis and chick dorsal dermis resulted in the growth of scale primordia (no feathers could form) arranged in the feather pattern [8] and recombinations of mouse epidermis and feather dermis produced hairs. How is the information for making feathers or scales in different regional domains stored within an individual organism? Can this regional specificity be perturbed? In nature, ptilopody (feathers on foot scales) exists in certain strains of chickens, suggesting that the presence of feathers on what is normally a scale-producing region is a heritable trait. This implies that there is a genetic basis determining the regional specificity of skin appendages in the bird. Certain concentrations of bromodeoxyuridine can produce a similar phenotype, suggesting changes in the gene-expression pattern [40]. Retinoic acid can cause feather formation on all the three types of foot scales, suggesting a chemical basis for the conversion [41••]. On the other hand, retinoic acid added to cultured feather explants converted feather buds into scale-like appendages [42]. Regional differences of the Hox expression pattern on chicken skin led us to propose that the skin Hox code is related to regional specificity of skin appendages [43•,44]. Retinoic acid indeed caused the expression pattern of Hox D13 in the foot to disappear, approximating it more to that of the feather dermis [44].

With the development of RCAS-mediated gene transduction, the ectopic expression of several genes was observed to produce interesting phenotypes when injected into the leg buds. A dominant negative form of the BMP receptor resulted in ptilopody of the scuta and scutella, but not reticulate scales [45••] —suggesting that BMP may be one of the suppressors of feather formation for the leg dermis. β-catenin is another important molecule that can cause the outgrowth of feathers from the scale epidermis [46••] and apteric skin [47•]. Analysis showed that, in each case, the scale epidermis became activated during the conversion to feathers, and the distribution of molecular markers such as SHH, NCAM and Tenascin-C were characteristic of feather buds. The ectopic feathers form follicle sheaths, dermal papillae and barb ridges [46••]. In mouse, LEF1, a β-catenin molecular partner, caused hair to grow out from the gum region [48], and β-catenin caused new hair formation [49••]. These results suggest that activation of the β-catenin pathway can activate the versatile appendage-forming potentials of epidermal cells. Notch and its ligands are known to be involved in cell-fate decisions and the misexpression of Delta-1 in the leg bud also caused feather- like outgrowths from scales [50].

These results suggest that the determination of feathers, scales and other integument appendages is based on tissue interactions and involves morphogenesis and differentiation. Tilting the equilibrium among molecular pathways can lead to different morphological phenotypes. The next challenge is understand the molecular cascades that regulate the cellular events behind each morphogenetic process (Figure 2).

Oh wait, the paper's authors were able to conduct experiments in which different tissues could be directed to produce feathers or scales, depending upon the presence or absence of particular, well-defined signalling gene products. By the way, the genes in question are found right across vertebrate taxa, and indeed many of them appear in invertebrate taxa as well (β-catenin, bmp, wnt and fgf being products of entire gene families found in organisms ranging from Caenorhabditis elegans to humans).

Looks like once again, the scientists know more, as a consequence of their diligent research, than creationists can even fantasise about knowing.

Wortfish wrote:Birds are warm-blooded, reptiles are cold-blooded.

The literature on this topic is also pretty extensive. Plus, mammals are warm-blooded, yet a large body of evidence exists that mammals arose from reptilian ancestors. The requisite ancestors stretch back to the Late Permian, and thus the onset of mammal evolution pre-dates that of bird evolution by about 100 million years. Given that I have some JavaScript debugging to attend to, I'll save this for another time.

Wortfish wrote:Birds have lungs and femurs specialised for flight, reptiles do not.

The literature on this topic is also pretty extensive.

Plus, none of your simplistic attempts at "gotcha's" explains why, as I stated earlier, birds contain genes for Archosaurian teeth. Nor does it have any answer to those papers I provided above on feather evolution.