" Tetrapods evolved " . Really ?

" Tetrapods evolved " . Really ?  

https://reasonandscience.catsboard.com/t2219-tetrapods-evolved-really

I thought  how much brainpower was required to program and make these robots from Boston dynamics. In the natural world , according to proponents of naturalism, the required coordination and invention of new limbs was due just to random natural processes. That made me have a closer look what mainstream scientific papers have to say about the subject. How did the first limbs  of tetrapods emerge ? What mechanism is required to grow body parts like legs, and how do proponents of evolution explain the arise of tetrapods ?

According to proponents of evolution, tetrapods arose from a lineage of fish. This kind of dramatic change over time is called macroevolution.
The transition from life in water to life on land would have necessitated dramatic structural changes of the whole body to withstand the increased effects of gravity, amongst other new requirements.
Many aspects of tetrapod origins remain elusive. Its supposed evolution has generated great interest, but the earliest phases of their history are poorly understood. Recent studies have questioned long-accepted hypotheses about the origin of the pentadactyl limb, the phylogeny of tetrapods and the environment in which the first tetrapods lived.
The ‘earliest’ known tetrapods with feet and legs are now thought to have been aquatic animals; proponents of evolution  therefore argue that feet and legs evolved in a shallow water environment and were only later co-opted for use on the land.

Most discussions of the topic concentrate to elucidate if the fossil record permits to find transitional forms that permit infer a water to land transition. Not only are there hudge gaps, but the idea bears big problems conceptually, and as a whole.

https://reasonandscience.catsboard.com/t1808-transition-from-water-to-land-dilemma?highlight=land

Moreover, as Behe explained nicely : In order to say that some function is understood, every relevant step in the process must be elucidated. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as the arise of tetrapods must include  how the transition occurred on a molecular explanation. It is no longer sufficient  for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant. So is the fossil record. It does not matter whether or not the fossil record is consistent with evolutionary theory, any more than it mattered in physics that Newton’s theory was consistent with everyday experience. The fossil record has nothing to tell us about, say, whether or how the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step. Neither do the patterns of biogeography matter, or of population genetics, or the explanations that evolutionary theory has given for rudimentary organs or species abundance.

So rather than stick to anatomy comparisons of fossils that might bear some similarity that could be interpreted as intermediates and evolution of tetrapod limbs from fish fins , let us try to elucidate how significant the  functional and morphological shift was it in terms of the underlying genetic mechanisms . The fossil record provides insight into supposed  morphological changes. However, to understand the underlying mechanisms, we must peer into the gene regulatory networks of living vertebrates.

Do new anatomical structures arise de novo, or do they evolve from pre-existing structures? Advances in developmental genetics, palaeontology and evolutionary developmental biology have recently supposedly  shed light on the origins of  the structures that most intrigued Charles Darwin, including  tetrapod limbs. According to proponents of evolution, structures arose by the modification of pre-existing genetic regulatory circuits.

My comment: The genetic program instructs how to make new structures, but that program must be precisely programmed, and  the genetic regulatory circuits need also to be programmed . That is, two separate programs need to emerge, that is 1. the program which defines the physical form and structure, and 2. the program which instructs  where to find the genetic information in the genome, and when to express it during development, that is in the right sequence. That are different layers of information, which must exist fully developed in order to make the new anatomical parts  in question. 

The instructions that control when and where a gene is expressed are written in the sequence of DNA bases located in the regulatory region of the gene. These instructions are written in a language that is often called the ‘gene regulatory code’. This code is read and interpreted by proteins called transcription factors that bind to specific sequences of DNA (or ‘DNA words’) and increase or decrease gene expression. Changes in gene expression between species could therefore be due to changes in the transcription factors and/or changes in the instructions within the regulatory regions of specific genes.

In order for communication to happen, 1. The sequence of DNA bases located in the regulatory region of the gene is required , and 2. transcription factors that read the code. If one of both is missing, communication fails, the gene that has to be expressed, cannot be encountered, and the whole procedure of gene expression fails. This is a irreducible complex system. The gene regulatory code could not arise in a step-wise manner either, since if that were the case, the code has only the right significance if fully developed.  Thats a example par excellence of intelligent design.

https://reasonandscience.catsboard.com/t2220-shannons-theory-of-information

During vertebrate limb development, Hoxd genes are transcribed in two temporal phases; an early wave controls growth and polarity up to the forearm and a late wave patterns the digits. In this issue of Developmental Cell, Tarchini and Duboule (2006) report that two opposite regulatory modules direct early collinear expression of Hoxd genes.

Question : how could natural mechanisms have programmed and directed the right temporal phases of gene transcription of the right genes,  and early wave control ? Furthermore, the limbs develop at the right place, the right coordinates and positional information is required, they could develop anywhere on the body. Did natural mechanisms find out about the right place by trial and error ? There were myriads of positions possible to add the limb. How could the right and precise coordination of axial position be achieved by mutations ? 


The problem is that nature has too many options and without design couldn’t sort them all out. Natural mechanisms are too unspecific to determine any particular outcome. Mutation and natural selection could theoretically form a new complex morphological feature like a  leg or a limb with the right size and form , and arrange to find out the right body location to grow them , but it could  also produce all kinds of other new body forms, and grow and attach them anywhere on the body, most of which have no biological advantage or are most probably deleterious to the organism. Natural mechanisms have no constraints, they could produce any kind of novelty. Its however that kind of freedom that makes it extremely unlikely that mere natural developments provide new specific evolutionary arrangements that are advantageous to the organism.  Nature would have to arrange almost a infinite number of trials and errors until getting a new positive  arrangement. Since that would become a highly  unlikely event, design is a better explanation. 

Going over through several mainstream scientific papers, i have not come across one of them, that were able to provide a detailed description how exactly the morphological transition could have occurred through evolution.

Some biologists have also envisioned special mutations in regulatory homeobox or "Hox" genes, where simple mutations might be able to make large developmental changes in an organism which might case a radically different phenotype. However, manipulating "Hox" genes does little to solve the problem of generating novel functional biostructures, for making large changes in phenotype are rarely beneficial. Hox gene mutations may be a more simple mechanism for generating large change, but they also do not escape the problem of the "hopeful monster":"The drawback for scientists is that nature's shrewd economy conceals enormous complexity. Researchers are finding evidence that the Hox genes and the non-Hox homeobox genes are not independent agents but members of vast genetic networks that connect hundreds, perhaps thousands, of other genes. Change one component, and myriad others will change as well--and not necessarily for the better. Thus dreams of tinkering with nature's toolbox to bring to life what scientists call a "hopeful monster"- such as a fish with feet--are likely to remain elusive."Furthermore, many biologists forget when invoking Hox gene mutations that Hox genes can only re-arrange parts which are already there--they cannot create truly novel structures.

Casey Luskin : Hox mutations will never create new "body part genes", and thus cannot add truly new phenotypic functions into the genome, and at best we are left with the quandaries associated with "pre-adaptation". The majority of evolutionary change must take place through evolving new "body part genes", which Hox mutations cannot do. One reviewer in Nature recognizes this fact:"Schwartz ignores the fact that homeobox genes are selector genes. They can do nothing if the genes regulated by them are not there. It is these genes that specify in detail the adaptive structure of the organs. To be sure, turning on a homeobox gene at the wrong place can result in the appearance of an ectopic organ, but only if the genes for that organ are present in the same individual. It is totally wrong to imply that an eye could be produced by a macromutation when no eye was ever present in the lineage before.


Darwins doubt, pg.239
WHAT ABOUT HOX GENES? Hox (or homeotic) genes regulate the expression of other protein-coding genes during the process of animal development. Some biologists have likened them to the conductor of an orchestra who plays the role of coordinating the contributions of the players. And because Hox genes affect so many other genes, many evo-devo advocates think that mutations in these genes can generate large- scale changes in form.

But can mutations in Hox genes transform one form of animal life—one body plan—into another? There are several reasons to doubt that they can.
First, precisely because Hox genes coordinate the expression of so many other different genes, experimentally generated mutations in Hox genes have proven harmful.  in fruit flies "most mutations in homeotic [Hox] genes cause fatal birth defects." In other cases, the resulting Hox mutant phenotype, while viable in the short term, is nonetheless markedly less fit than the wild type. For example, by mutating a Hox gene in a fruit fly, biologists have produced the dramatic Antennapedia mutant, a hapless fly with legs growing out of its head  where the antennae should be.  

https://reasonandscience.catsboard.com/t2077-hox-genes


Recently i saw following youtube video : https://www.youtube.com/watch?v=M8YjvHYbZ9w




The evolution of tetrapods

Evolutionary patterns in early tetrapods. I. Rapid initial diversification followed by decrease in rates of character change
two aspects of tetrapod diversification allow us to contrast predictions of intrinsic constraint (i.e. developmental or genetic) or ecological restriction (i.e. filling of general ecospace) models for reducing rates of morphological change. First, Ruta & Coates's (2006) results suggest that post-Devonian tetrapods evolved from a single Late Devonian/Early Carboniferous taxon. This phylogenetic ‘bottleneck’ (sensu Jablonski 2002) yields a second radiation into similar (i.e. semi-aquatic) ecospace; thus, if ecology alone is responsible for rates of morphological change, then we expect Early Carboniferous rates to mimic Devonian rates; however, if intrinsic constraints accumulated in the interim, then we do not. Second, the diversification of stem- and basal crown-amniotes in the Late Carboniferous represents a second invasion into a new ecospace (i.e. fully terrestrial environments). If ecological restrictions affect rates of morphological change more strongly than intrinsic constraints do, then we expect to see additional high rates of change of tetrapod diversification. Conversely, if intrinsic constraints accumulated prior to this radiation, then we might see increased disparity due to diversification, but no increase in rates.

The Fish–Tetrapod Transition 

Tetrapods, for example, arose from a lineage of fish. This kind of dramatic change over time is called macroevolution.

The Devonian is often referred to as the “age of fishes” because of the astonishing diversity displayed by aquatic vertebrates during this interval. However, as is clear, terrestrial plants had evolved by the Ordovician, and insects began exploiting resources on land from the Silurian or earliest Devonian; the vertebrates would not be far behind. Over the past 20 years, a series of important papers have shed light on the sequence of character evolution associated with the first land-living, limbed vertebrates—the tetrapods



Figure 18.13 shows four Late Devonian vertebrates that span the fish-totetrapod transition. All are sarcopterygians (lobe-fin bony fish) characterized by a single proximal bone in the fin/limb recognized as the humerus (forelimb) or femur (hindlimb). In addition to modifying the fin into a limb, the transition from life in water to life on land necessitated structural changes to withstand the increased effects of gravity. Tetrapods such as Acanthostega show well-developed joints between consecutive vertebrae (zygapophyses) that are absent in aquatic taxa like Eusthenopteron, as well as enlarged rib attachments. Moreover, the pelvis was solidly connected to the vertebral column by means of novel sacral ribs. Many physiological changes undoubtedly also occurred (e.g., respiration, osmoregulation), but these are extremely difficult to gauge in the fossil record. The loss of fin rays (lepidotrichia) and their replacement by digits (Figure 18.14)



is a tetrapod hallmark, but there is increasing evidence that the earliest tetrapods spent much of their time in water (Coates et al. 2008; Pierce et al. 2012). For example, Acanthostega retained a caudal fin and had a fully formed gill skeleton. Equally surprising is the knowledge that many presumed tetrapod features were already present in derived aquatic sarcopterygians (such as Tiktaalik), like the loss of dorsal and anal fins and a flattened skull with dorsally facing orbits. Fossils of Acanthostega, Ichthyostega, and other early tetrapods were recovered from rocks interpreted as being freshwater, estuarine, or marginal marine in origin. The lack of tetrapod fossils from marine rocks helps to eliminate some prospective habitats for the origin of the group, but many aspects of tetrapod origins remain elusive. Why did tetrapods invade dry land? The classic theory is largely based on the ecology of the modern Australian lungfish, which is known to move between ponds that shrink during the dry season. Climate models suggest that the Late Devonian was substantially warmer than today, but also important were untapped foods available on land, in the form of insects, which were in turn feeding on Devonian plants. The recent discovery of tetrapod trackways from the Early Devonian of Poland (Niedzwiedzki et al. 2010; see Figure 18.4) suggests that paleontologists may need to look in rocks approximately 18 million years older than the Late Devonian rocks that currently provide the bulk of tetrapod body fossils.

Recent work has done much to illuminate the details of the origin of tetrapods. We can now see that it was a fairly gradual affair, with the transition from aquatic to fully terrestrial life stretching across the upper part of the stem group from the Panderichthys node to the base of the crown group and occupying a time interval of about 15-20 million years from the late Middle Devonian to the Early Carboniferous. However, within this extended period of change lies a brief pulse of much more rapid and dramatic morphological evolution, the traditionally recognised “origin of tetrapods”, which occupied about 5 million years and corresponds to the internode between Panderichthys and Elginerpeton. This phase of rapid change was probably driven by selection pressure for terrestrial or extreme shallow-water competence, but it is possible that pleiotropic effects due to linked gene expression patterns were also involved in some of the changes. Phylogenetic and developmental genetic data can at present only be synthesised (in a preliminary manner) in relation to the evolution of limbs.

2) Evolutionary Analysis (5th Edition) Jon C. Herron (Author), Scott Freeman page 701

The fossil record of ‘early’ tetrapods: evidence of a major evolutionary transition?

Summary

According to evolutionary theory, the origin of tetrapods from a fish-like ancestor during the Devonian Period was one of the major events in the history of life on earth. The ‘drying pond’ hypothesis was proposed to explain the selection pressures behind the transition. According to this hypothesis, the tetrapods evolved as fishes became progressively better adapted to terrestrial conditions during prolonged episodes of drought. Recently, however, the assumption that feet and legs evolved to facilitate life on the land has been called into question. The ‘earliest’ known tetrapods with feet and legs are now thought to have been aquatic animals; proponents of evolution  therefore argue that feet and legs evolved in a shallow water environment and were only later co-opted for use on the land. This paper reviews the radical changes in thinking about the fish-tetrapod transition that have taken place in the evolutionary community. It also considers the chimeromorphic nature of Devonian tetrapods and fishes, and offers some critical comments on the evolutionary interpretation of their fossil record.


Proponents of evolution believe that tetrapods—i.e. vertebrates with four limbs—were the first animals to move on to the land, having evolved from a fish ancestor during the Devonian period (conventionally 408 to 360 million years ago). The fossil record of Devonian tetrapods is often presented as compelling evidence of this major evolutionary transition.¹ Science writer Carl Zimmer has written a popular book, At the Water’s Edge,² which purports to show how life came ashore (i.e. how fish evolved into tetrapods) and then went back to the sea (i.e. how land mammals gave rise to the whales). A more technical presentation was written recently by Jenny Clack, Reader in Vertebrate Palaeontology and Senior Assistant Curator of the University Museum of Zoology, Cambridge. EntitledGaining Ground: The Origin and Evolution of Tetrapods,³ it begins with these words:

‘About 370 million years ago, something strange and significant happened on Earth. That time, part of an interval of Earth’s history called the Devonian Period by scientists such as geologists and paleontologists, is known popularly as the Age of Fishes. After about 200 million years of earlier evolution, the vertebrates—animals with backbones—had produced an explosion of fishlike animals that lived in the lakes, rivers, lagoons, and estuaries of the time. The strange thing that happened during the later parts of the Devonian period is that some of these fishlike animals evolved limbs with digits—fingers and toes. Over the ensuing 350 million years or so, these so-called tetrapods gradually evolved from their aquatic ancestry into walking terrestrial vertebrates, and these have dominated the land since their own explosive radiation allowed them to colonize and exploit the land and its opportunities. The tetrapods, with their limbs, fingers, and toes, include humans, so this distant Devonian event is profoundly significant for humans as well as for the planet.’⁴

Indeed, according to the cladistic framework that now dominates evolutionary systematics, humans are not simply descended from fish—they are fish! Clack states:

‘Although humans do not usually think of themselves as fishes, they nonetheless share several fundamental characters that unite them inextricably with their relatives among the fishes … Tetrapods did not evolve from sarcopterygians [lobe-finned fishes]; they are sarcopterygians, just as one would not say that humans evolved from mammals; they are mammals.’⁵

In this paper I will critically examine the fossil record of ‘early’ tetrapods and discuss the way in which older evolutionary views of their origin have been overturned in the last two decades. I will also consider the mosaic distribution of characters that we observe in Devonian tetrapods and fishes, the problems that it poses for evolutionary theory, and how it might be understood in a creationist framework.

The ‘drying pond’ hypothesis

Many evolutionary scenarios have been proposed to explain the origin of tetrapods. Most of them were developed to answer the question, ‘Why did fish leave the water and come onto the land?’ The early theories usually focused on the environmental setting and selection pressures behind the transition. Tetrapods were thought to have evolved during the Devonian, a period associated in many parts of the world with sediments stained red by iron oxide. Classic red beds, such as the Siluro-Devonian rocks of Europe (the Old Red Sandstone) and their North American equivalents (the Catskill and Escuminac formations), have often been interpreted as the product of hot, semi-desert environments with seasonal wetness. This led many to speculate that an increasingly arid climate was a major influence on the evolution of air-breathing vertebrates. A classic paper by Barrell⁶ set the scene for much future discussion. He argued that the first tetrapods arose ‘under the compulsion of seasonal dryness’.⁷ Under such conditions, it was suggested, the air-bladder of certain fishes became progressively better adapted as an organ of respiration and the gills atrophied. The development of a new system of breathing allowed fishes to survive the drought conditions by moving between bodies of water. Those fishes with more limb-like appendages were better able to make the journey and this ultimately led to the evolution of limbs with digits. This became known as ‘the drying pond hypothesis’ and was popularized by the great vertebrate palaeontologist Alfred Sherwood Romer.⁸

Figure 1. Reconstruction of Ichthyostega, showing skull, vertebral column, and limbs, and its hind limb based on a specimen collected in 1987. Note the seven digits on the hind limb (from Clack).15

‘Early’ tetrapods from East Greenland

When Romer was popularizing the ‘drying pond’ idea, the earliest known tetrapods were Ichthyostega and Acanthostega from the Upper Devonian of East Greenland.Ichthyostega was first described by Säve-Söderbergh⁹ and then by Jarvik in a series of papers and a monograph.^10–12 Although the anatomy of Ichthyostega is known in considerable detail, its body proportions are uncertain because the fossil material comes from more than one individual. Ichthyostega is about one metre long with a broad, flat head, short, barrel-shaped body, stocky legs, large pelvic and pectoral girdles, and a rib cage with broad, overlapping ribs (Figure 1). It is very evidently a tetrapod, with limbs rather than fins. Nevertheless, Ichthyostega has some fish-like characteristics, including a lateral line system and a tail with bony fin rays. Early reconstructions portrayed Ichthyostega as a semi-aquatic creature but most later ones depicted it as a predominantly terrestrial animal (e.g. Jarvik¹³). As recently as 1988, a major vertebrate palaeontology text described Ichthyostega as a fairly typical land animal with the usual complement of five digits on the hind limb.¹⁴ The second Devonian tetrapod from East Greenland was Acanthostega.^9,10 For many years this animal was known only from two partial skull roofs, but these were enough to mark it out as different from Ichthyostega.

The search for evolutionary ancestors

Proponents of evolution  sought the ancestry of the tetrapods among the lobe-finned fishes. Although the lobe-fins are dominant in the fossil fish faunas of the Palaeozoic (conventionally 590 to 248 million years ago), they are represented today by only four surviving genera (the coelacanthLatimeria and three genera of lungfish). In 1892, Cope and others argued that tetrapods had evolved from the crossopterygians, the group of lobe-fins that includes the coelacanths.¹⁶ Various crossopterygians were proposed as the ‘model ancestor’, including Sauripteris^17,18 andOsteolepis.¹⁹ However, most attention settled upon Eusthenopteron, from Escuminac Bay in Quebec, Canada. This is the fish that was commonly illustrated, in popular books on fossils, as hauling itself up onto Devonian riverbanks (e.g. Owen²⁰).
Nevertheless, there was evidently a substantial discontinuity in the fossil record between terrestrial vertebrates like Ichthyostega and their presumed ancestors. This was reflected in creationist treatments of the problem²¹ and acknowledged by evolutionists, such as Carroll²² who wrote:

‘We have not found any fossils that are intermediate between such clearly terrestrial animals and the strictly aquatic rhipidistians described in the previous chapter.’

[th]Taxon[/th][th]Stratigraphic unit[/th][th]Age[/th][th]Location[/th][th]Material[/th][th]Reference(s)[/th]

Pederpes	Ballagan Fm	Tournaisian	Scotland	Skull, almost complete articulated skeleton	23
Sinostega	Zhongning Fm	Famennian	Ningxia Hui, China	Incomplete left mandible	24
Tulerpeton	Khovanshchina Beds	Famennian	Tula Region, Russia	Fore and hind limbs, partial pectoral and pelvic girdles, skull fragments	25–28
Ventastega	Ketleri Fm	Famennian	Latvia	Skull fragments, girdle fragments	29
Acanthostega	Britta Dal Fm	Famennian	East Greenland	Skulls, articulated skeletons	9,10,30–36,44,50
Ichthyostega	Aina Dal Fm Britta Dal Fm	Famennian	East Greenland	Skulls, skeletal elements, some articulated	9–12,44
Hynerpeton	Catskill Fm	Famennian	Pennsylvania, USA	Pectoral girdle, skull fragments	37,38
Densignathus	Catskill Fm	Famennian	Pennsylvania, USA	Lower jaw	38
Metaxygnathus	Cloghnan Shale	Famennian	New South Wales, Australia	Lower jaw	39
Elginerpeton	Scat Craig Beds	Frasnian	Scotland	Ilia, limb bones, skull and pectoral girdle fragments	40–42
Obruchevichthys	Ogre Beds	Frasnian	Latvia	Lower jaw fragments	40
Livoniana	Gauja Fm	Givetian	Latvia	Lower jaw fragments	43

Table 1. ‘Early’ tetrapods and so-called ‘near tetrapods’. Most are represented by single specimens; Acanthostega is unique in that it represents a stratigraphic range. Givetian is a subdivision of the Middle Devonian, Frasnian and Famennian are subdivisions of the Upper Devonian, and Tournaisian is a subdivision of the Lower Carboniferous.

Aquatic tetrapods challenge the ‘drying pond’ hypothesis

Since 1990 our knowledge of ‘early’ tetrapods has been greatly expanded, with many new taxa being described. Fossil material is now known from Scotland, Greenland, Latvia, the USA, Australia, Russia, and China (Table 1).^23–43 Furthermore, our understanding of the Greenland tetrapods has been revolutionized by the discovery of new material. As a consequence, a major re-evaluation of tetrapod origins has taken place, and almost every aspect of the ‘drying pond’ hypothesis has had to be discarded.

Figure 2. Acanthostega in a swimming posture (from Clack).46

The fatal blow to the ‘drying pond’ hypothesis has been the realization that the Devonian tetrapods were predominantly aquatic in habit. New ichthyostegid material, including a well-preserved and articulated hind limb, collected by an expedition to East Greenland in 1987, revealed that Ichthyostega was polydactylous, with seven digits on the hind limb (Figure 1).⁴⁴ This was a very surprising discovery because pentadactyly had been assumed to be the normal condition in ‘early’ tetrapods. Furthermore, the flattened bones and inflexible ankle of the hind limb suggests that it was more like the paddle of an elephant seal than the leg of a terrestrial animal.⁴⁵ It appears that the earliest reconstruction of Ichthyostega as a creature at home in the water was more accurate than later ones portraying it on land.
Acanthostega is also much more completely known as a result of material collected by the 1987 expedition, including the first postcranial remains.^47,48 It was a smaller animal than Ichthyostega and its teeth suggest that it had a different diet. Several articulated specimens were found in a single lens of rock, interpreted as a possible flash flood deposit.⁴⁹ The remarkable preservation meant that some delicate structures, not often preserved in fossil tetrapods, are known inAcanthostega. The gill skeleton was fish-like⁵⁰ and it has been suggested that Acanthostega had internal gills somewhat similar to those of the Australian lungfish (Neoceratodus). Acanthostega had a tail with fin rays, even larger than that of Ichthyostega (Figure 2). The fin rays also extended further beneath the tail, in similar fashion to those of a lungfish, suggesting that Acanthostega was a thoroughly aquatic creature. This conclusion is supported by the morphology of the fore and hind limbs which are difficult to interpret as load-bearing structures; rather, they appear to be designed for swimming. As with Ichthyostega, perhaps the most extraordinary feature was the number of digits. An articulated fore limb revealed eight digits in a paddle-like arrangement (Figure 3). Clack⁵¹ speculates that they may have been enclosed in some kind of webbing.

Figure 3. The left forelimb of Acanthostega, showing the eight digits (from Clack).52

Most evolutionists had assumed that the origin of limbs with digits was synonymous with the vertebrate invasion of the land. This led to the popular ‘conquest of the land’ idea, typified by artistic reconstructions and museum displays of fish crawling out of Devonian pools. However, the latest thinking about the aquatic or semi-aquatic nature of the Devonian tetrapods has led modern-day evolutionists to reject this assumption. They now argue that the key tetrapod characters evolved for a shallow-water existence and were only later co-opted for terrestrial use. The new generation of Darwinists dismisses the ‘drying pond’ hypothesis as untestable story-telling, and increasingly relies on cladistics as an alternative framework for understanding the transition. The cladistic approach to the fish-tetrapod transition focuses on determining the sequence of acquisition of key tetrapod characteristics, from which inferences are drawn about the nature of the transition.⁵³ We should recognize, however, that the cladistic methodology is inherently Darwinian and assumes from the outset the continuity of life. By its very nature, cladistics is insensitive to the discontinuities which creationists believe characterize living things.⁵⁴

Other problems with the ‘drying pond’ hypothesis

The drying pond hypothesis has other problems.⁵⁵ For instance, it is recognized that red beds are not necessarily indicators of arid climates:

‘The red bed problem has been extremely controversial, with marked differences of opinion, possibly due to the fact that the term “red bed” is a catchall for many sedimentary types produced under different conditions, the only common feature of them being the red color.’⁵⁶

Modern red beds develop in the oxidizing conditions of the low latitude tropics (e.g. the Amazon Basin). Such environments are characterized by monsoonal rainfall, not arid conditions. Another problem is that, even if the red beds were laid down under conditions of semi-aridity, evolutionists cannot assume that the tetrapods arose in such environments, for the simple reason that many Devonian sediments are not red beds. Some are interpreted as river, lake, or near-shore sediments rich in organic matter, suggesting nearby forests.⁵⁷
Furthermore, a survey of modern fishes that leave the water to spend time on land⁵⁸ affords no support for the ‘drying pond’ hypothesis. There is no association between those that leave the water and those that possess digit-like fins. For example, eels undertake long journeys overland but they have nothing that could be described as digit-like appendages. Indeed, most of the fishes that possess digit-like structures are deep water species or habitual bottom dwellers, such as the Sargassum frogfish.

New views on tetrapod ancestry

There have also been changes of opinion about which group of fishes is closest to the ancestry of tetrapods. Eusthenopteron is no longer regarded as the model ancestor. Depictions showing this fish emerging onto dry land owed more to evolutionary presuppositions than evidence. Eusthenopteron was a rather undistinguished fish with no obvious adaptations to terrestrial life; tetrapod-like behaviour was attributed to it simply because there was no better candidate to fill the role of tetrapod ancestor. The true lifestyle of Eusthenopteron seems to have been that of a lurking aquatic predator, somewhat similar to the modern pike (Esox).
Attention is now focused on the formerly more obscure lobe-finned fishes, Panderichthys and Elpistostege. Until recently, these two genera were united in a family called the panderichthyids, but evolutionists now believe that they are not uniquely related to each other.⁵⁹ Fossil material from Latvia and Canada shows that these fish were more tetrapod-like than other lobe-fins. Indeed, based on a partial skull roof,Elpistostege was originally described as a tetrapod.⁶⁰ Although there has been dissent,^61,62 these genera are increasingly regarded by evolutionists as the closest known relatives of tetrapods.^63–65 The latest work by Ahlberg et al.⁴³ indicates that Elpistostege is even more tetrapod-like than Panderichthys. These fish have crocodile-like skulls with dorsally placed eyes, straight tails, and slightly flattened bodies without dorsal or anal fins (see Figure 4). Like tetrapods, but unlike all other fishes, they also have frontal bones in the skull roof. LikeEusthenopteron, they seem designed for life as shallow-water predators.

Figure 4. Panderichthys, an Upper Devonian lobe-finned fish regarded by evolutionists as close to the ancestor of tetrapods (from Clack).59

Chimeromorphs pose problems for evolutionary theory

Creationists and evolutionists have observed that many organisms, both fossil and living, exhibit a mosaic distribution of character traits. Parker⁶⁶ put it this way:

‘Each created kind is a unique combination of traits that are individually shared with members of other groups.’

Stephen Jay Gould called such organisms ‘mosaic forms’ or ‘chimeras’⁶⁷ while Kurt Wise^68,69 calls them chimeromorphs. The duck-billed platypus (Ornithorhynchus anatinus), for instance, has features of both mammals (hair, milk production) and reptiles (egg-laying). Perhaps the best-known fossil example is Archaeopteryx, which combines feathers with teeth and wing claws. In fact, a mosaic pattern of character distribution is seen in many other fossil organisms. For instance, Woodmorappe⁷⁰ recently drew attention to the chimeric nature of the pakicetids, a group of terrestrial artiodactyls with a whale-like inner ear.
This observation seems to apply to the Devonian tetrapods and fishes considered in this article. For example, Daeschler et al. noted that:

‘Devonian tetrapods show a mosaic of terrestrial and aquatic adaptations.’⁷¹

Some of the fishes possess tetrapod-like characters while the tetrapods have fish-like features. Evolutionists interpret mosaic organisms like these as evolutionary intermediates linking major groups. However, Wise⁷² makes an important point against this interpretation:

‘Although the entire organism is intermediate in structure, it’s the combination of structures that is intermediate, not the nature of the structures themselves. Each of these organisms appears to be a fully functional organism full of fully functional structures.’

Evolutionary theory might lead us to expect examples of intermediate structures, but there is nothing intermediate about, for example, the internal gills of Acanthostega, its lateral line system, or its limbs. They are fully developed and highly complex. What is unusual is their combination in a single organism. Intelligent design offers an alternative understanding of this widespread pattern. The Devonian tetrapods are thought to have lived a predatory lifestyle in weed-infested shallow water. They were therefore equipped with characteristics appropriate to that habitat (e.g. crocodile-like morphology with dorsally placed eyes, limbs and tails made for swimming, internal gills, lateral line systems). Some of these features are also found in fishes that shared their environment.
The mosaic pattern makes it difficult to identify organisms or groups of organisms that possess the ‘right’ combination of characters to be considered part of an evolutionary lineage. Consider the tetrapod-like lobe-fins Panderichthys and Elpistostege. Despite their appearance, these fish have some unique characters (such as the design of the vertebrae) that rule them out as tetrapod ancestors. At best, evolutionists can only claim that they are a model of the kind of fish that must have served as that ancestor. The same problem is encountered with the Devonian tetrapods. For example, Ichthyostega is described as ‘a very strange animal, and parts of it are like no other known tetrapod or fish’.⁷³ Similarly, the shoulder girdles of the Devonian tetrapods ‘are not obviously halfway in structure between those of fishes and those of later tetrapods but have some unique and some unexpected features’.⁷⁴ Another example is Livoniana, a so-called ‘near tetrapod’ known from two lower jaw fragments. It possesses a curious mixture of fish-like and tetrapod-like characteristics, but it also has up to five rows of teeth, a feature not seen either in the fishes from which it is thought to be descended nor the tetrapods into which it is said to be evolving.⁷⁵ That the mosaic distribution of characters can cause great confusion is exemplified by the recent discovery of Psarolepis, a fish from the Upper Silurian/Lower Devonian of China, which combines characters found in placoderms, chondrichthyans, ray finned fishes, and lobe-fins.⁷⁶

Additional problems with ‘early’ tetrapod evolution

Another problem is that the fossil record imposes tight constraints on the timing of the supposed transition. The earliest tetrapod fossils are found in late Frasnian sediments, but their presumed ancestors are hardly much older. To exacerbate the situation, the Frasnian ‘near tetrapods’ (Obruchevichthys, Elginerpeton, Livoniana) are already morphologically diverse at their first appearance.⁷⁷ Thus Darwinists are compelled to postulate a rapid burst of evolution in which radical changes must have taken place:

‘Panderichthys and Elpistostege flourished in the early Frasnian and are some of the nearest relatives of tetrapods. But tetrapods appear only about 5 to 10 million years later in the late Frasnian, by which time they were widely distributed and had evolved into several groups, including the lineage leading to the tetrapods of the Famennian. This suggests that the transition from fish to tetrapod occurred rapidly within this restricted time span.’⁷⁸

Second, key morphological transitions, such as the purported change from paired fins to limbs with digits, remain undocumented by fossils. Where appendages are known they are clearly either fish-like fins or digit-bearing limbs, not at some transitional stage from one to the other. At one time it was claimed that the pectoral fins of rhizodonts, a group of lobe-finned fish, were remarkably similar to tetrapod limbs, but following the description of Gooloogongia from the Famennian of New South Wales, Johanson and Ahlberg⁷⁹ have urged that they not be used as a model for the origin of tetrapod limbs. Furthermore, the pectoral fins of lobe-finned fish tend to be larger than the pelvic fins, whereas the Devonian tetrapods were ‘rear-wheel drive’ animals with larger hind limbs than fore limbs.⁸⁰ None of the recent fossil discoveries shed any light on this supposed reconfiguration.
Third, there are functional challenges to Darwinian interpretations. For instance, in fish the head, shoulder girdle, and circulatory systems constitute a single mechanical unit. The shoulder girdle is firmly connected to the vertebral column and is an anchor for the muscles involved in lateral undulation of the body, mouth opening, heart contractions, and timing of the blood circulation through the gills.⁸¹However, in amphibians the head is not connected to the shoulder girdle, in order to allow effective terrestrial feeding and locomotion. Evolutionists must suppose that the head became incrementally detached from the shoulder girdle, in a step-wise fashion, with functional intermediates at every stage. However, a satisfactory account of how this might have happened has never been given.

Conclusion

Recent discoveries have undoubtedly advanced our knowledge of Devonian tetrapods and future creationist discussions of tetrapod origins must take this into account. It is no longer sufficient for creationists to contrast Eusthenopteron with Ichthyostega and point to the large morphological gap between them. We need to have more to say. Nevertheless, the presumed transition from fish to tetrapods remains contentious. The data and their interpretation are a source of lively debate and ongoing controversy:

‘In the not-too-distant past, there was almost no fossil material, and ideas were based largely on informed guesswork. Speculation was intense, and as is often the case, in inverse proportion to the amount of data. To be truthful, there is still not much real data, so that speculation is still active, and whatever is concluded today may be overturned by the discovery of a new fossil tomorrow. That in some sense is to be hoped for, because only in that way can guesses be falsified and tested as scientific hypotheses.’⁸²

A robust rationale for concluding that the Upper Devonian tetrapods evolved from a fish ancestor, or that they gave rise to Carboniferous tetrapod lineages, is lacking. It is hoped that this paper may stimulate creationists to develop a fuller understanding of these remarkable creatures and their ecological and geological context.⁸³
Paul Garner has a B.Sc. (Hons) in Geology and Biology and is a Fellow of the Geological Society of London. He works full-time as a speaker and researcher with Biblical Creation Ministries in the UK. He is also a Committee Member of the Biblical Creation Society, co-editor of the BCS journal, Origins, and is on the Board of The Genesis Agendum, a charitable company promoting church and public awareness of the substantial historical and scientific evidence supporting the biblical record.

http://creation.com/the-fossil-record-of-early-tetrapods-evidence-of-a-major-evolutionary-transition

Ventastega curonica and the origin of  tetrapod morphology 1

The gap in our understanding of the evolutionary transition from fish to tetrapod is beginning to close thanks to the discovery of new intermediate forms such as Tiktaalik roseae. Here we narrowit further by presenting the skull, exceptionally preserved braincase, shoulder girdle and partial pelvis of Ventastega curonica from the Late Devonian of Latvia, a transitional intermediate form between the ‘elpistostegids’ Panderichthys and Tiktaalik and the Devonian tetrapods (limbed vertebrates) Acanthostega and Ichthyostega. Ventastega is the most primitive Devonian tetrapod represented by extensive remains, and casts light on a part of the phylogeny otherwise only represented by fragmentary taxa: it illuminates the origin of principal tetrapod structures and the extent of morphological diversity among the transitional forms.

Because of its phylogenetic position and character complement it is tempting to interpret Ventastega as a straightforward evolutionary intermediate, which represents with reasonable accuracy the character complement of the tetrapod stem lineage at a point on the internode between Tiktaalik and Acanthostega. However, this simple picture should be approached with a degree of caution. ANSP 21350 and Elginerpeton in particular (whether or not the latter taxon is taken to include the disputed humerus GSM 104536; refs 13, 38) show character combinations that are substantively different from those of Ventastega and Acanthostega without being obviously autapomorphic,
and both probably occupy deep positions in the phylogeny.




1) Ahlberg, Clack et al, “Ventastega curonica and the origin of tetrapod morphology,” Nature 453, 1199-1204 (26 June 2008) | doi:10.1038/nature06991. http://www.nature.com/nature/journal/v453/n7199/abs/nature06991.html

Early tetrapod evolution 1

Tetrapods include the only fully terrestrial vertebrates, but they also include many amphibious, aquatic and flying groups. They occupy the highest levels of the food chain on land and in aquatic environments. Tetrapod evolution has generated great interest, but the earliest phases of their history are poorly understood. Recent studies have questioned long-accepted hypotheses about the origin of the pentadactyl limb, the phylogeny of tetrapods and the environment in which the first tetrapods lived.

Molecular data on the origin of digits Molecular developmental biology can provide valuable data about the evolutionary history of the endoskeletal serial elements of limbs. The differentiation of the segments is determined by a combination of the expressions of several Hox genes that are also involved in the identity of the posterior segments of the body. Only genes located at the 59 end of the four tetrapod clusters (HoxA to HoxD, gene numbers 9 to 13) are expressed during limb development 8. By contrast to tetrapods, the zebrafish (Danio rerio), a teleost, possesses seven clusters, with HoxA to HoxC clusters being duplicated compared with the mouse (Mus musculus), but HoxD is not duplicated 9. HoxD11-13 genes are expressed in a biphasic sequence in amniotes: the first expression is restricted posteriorly, whereas the second expression forms an arch on the full width of the distal mesenchyme10 (Fig. 4a).



This second expression phase corresponds closely to the bent pattern of prechondrogenic condensations of the digital arch (Figs 5d and e)11



This bend of HoxD expression is absent in zebrafish fin bud development 12 (Fig. 4b). This pattern suggests that the extremity of the autopod (the digits) is located at the posterodistal extremity of the limb. However, the HoxA-11 gene does not show this bend: it is expressed in a distal position in the zebrafish (Fig. 4d), whereas it is expressed in a band at the transition between the zeugopod and the autopod in the mouse12 (Fig. 4c). This second pattern suggests that the autopod is at the distal extremity of the limb. Comparison of both expression patterns suggests that the digits are at the posterior extremity of the limb (Fig. 5e), but the hypothesis that digits are at the distal extremity (Fig. 5f) cannot be ruled out definitively. A limb with both phalanges and lepidotrichia would enable us to choose between these two hypotheses. If the proximo-distal axis of the limb is straight (Fig. 5f), the lepidotrichia should be distal to the phalanges; whereas if the limb is bent, lepidotrichia should be mostly anterior to the phalanges (Fig. 5e). The sarcopterigyan Sauripterus has putative phalanges and lepidotrichia that are continuous with each other (Fig. 3b)



suggesting that the proximo-distal axis is not bent. However, the homology of the distal endoskeletal elements of Sauripterus to phalanges is uncertain.

The timing of the conquest of land by vertebrates is also worth investigating. We still ignore whether several Devonian and Carboniferous taxa were primitively or secondarily aquatic, and, in many cases, we do not even know how terrestrial or aquatic these taxa were. Future investigations using new types of data (isotopic, paleohistological, etc.) are needed to clarify these issues.

1) http://max2.ese.u-psud.fr/epc/conservation/Publi/abstracta/AE_TREE2000.pdf

Fish to tetrapods1

Dawkins discusses the transition between sea creatures and land, which was an undoubted large gap spanning a long period of evolutionary time, and even had a name, “Romer’s Gap”, after the American paleontologist A.S. Romer (1894–1973):

“‘Romer’s Gap’ … stretches about 360 million years ago, at the end of the Devonian period, to about 340 million years ago, in the early part of the Carboniferous, the ‘Coal Measures.’ After Romer’s Gap, we find unequivocal amphibians crawling through the swamps, a rich radiation of salamander like creatures … Before that, however, was Romer’s Gap. And before his gap, Romer could see only fish, lobe-finned fish, living in water. Where were the intermediates, and what led them to venture out on to the land.” (pp. 164–5)

Indeed, the evolution of land limbs and life on land in general requires many changes, and the fossil record has no evidence of such changes. Geologist Paul Garner writes: “There are functional challenges to Darwinian interpretations. For instance, in fish the head, shoulder girdle, and circulatory systems constitute a single mechanical unit. The shoulder girdle is firmly connected to the vertebral column and is an anchor for the muscles involved in lateral undulation of the body, mouth opening, heart contractions, and timing of the blood circulation through the gills.  However, in amphibians the head is not connected to the shoulder girdle, in order to allow effective terrestrial feeding and locomotion. Evolutionists must suppose that the head became incrementally detached from the shoulder girdle, in a step-wise fashion, with functional intermediates at every stage. However, a satisfactory account of how this might have happened has never been given.”

Yet some recent discoveries are alleged to have filled this gap.

Ichthyostega and Acanthostega

Dawkins discusses these two ‘intermediates’, although they have fully-formed pelvic girdles and limbs, unlike the Eusthenopteron, a lobe-finned fish. But who was the predecessor of whom? It depends on which characteristic one looks at: e.g. Ichthyostega’s skull seems more fish-like than Acanthostega’s, but its shoulder and hips are more robust and land-animal–like. Ichthyostega is allegedly the more amphibian-like, but Acanthostega possesses two ‘amphibian’ features that Ichthyostega does not. Indeed, even according to evolutionary ‘dating’, they are contemporaries



Furthermore, Panderichthys, which Dawkins describes as “slightly more amphibian-like, and slightly less fish-like, than Eusthenopteron” (p. 168 ), is dated earlier. And even the limbed creatures predate the fully-fish Coelacanth. Dawkins also notes the unusual digit numbers: Acanthostega had eight, while Ichthyostega had seven (pp. 167–8 ). He tries to wave away this contradiction:

“It seems that the early tetrapods enjoyed more freedom to experiment than we have today. Presumably at some point the embryological processes fixed upon five, and a step was taken that was hard to reverse. Although, admittedly, it is not as hard as all that. There are individual cats, and indeed humans, who have six toes. The extra toes probably arose from a duplication error in embryology.” (p. 167 )

But still, proponents of evolution often appeal to the common pentadactyl 5-digit pattern as evidence for their common ancestry from a 5-digited creature. Yet the nearest creatures they have to a common ancestor did not have five digits!

Tiktaalik

Dawkins is delighted with the discovery of Tiktaalik roseae, supposedly closing a gap between Panderichthys and Acanthostega: “Tiktaalik is the perfect missing link—perfect, because it almost exactly splits the difference between fish and amphibian, and perfect because it is missing no longer.” (p. 169)

Dawkins is following the infectious enthusiasm of evolutionary palaeontologists who claimed that this is “a link between fishes and land vertebrates that might in time become as much of an evolutionary icon as the proto-bird Archaeopteryx.” But how intermediate is it really? One of those enthusiastic palaeontologists cited above, Jennifer Clack (University of Cambridge, UK), admitted: “There remains a large morphological gap between them and digits as seen in, for example, Acanthostega: if the digits evolved from these distal bones, the process must have involved considerable developmental repatterning. … “Of course, there are still major gaps in the fossil record. In particular we have almost no information about the step between Tiktaalik and the earliest tetrapods, when the anatomy underwent the most drastic changes, or about what happened in the following Early Carboniferous period, after the end of the Devonian, when tetrapods became fully terrestrial.” Indeed, Tiktaalik’s fins that are supposed to have become legs were not connected to the main skeleton, so could not have supported its weight on land. The discoverers claim that they could have helped to prop up the body as the fish moved along the sea bottom, but proponents of evolution had similar high hopes for the coelacanth fin. However, when a living coelacanth (Latimeria chalumnae) was discovered in 1938, the fins later turned out not to be used for walking but for deft maneuvring when swimming.

Thus all the claims about Tiktaalik are mere smokescreens, exaggerating mere tinkering around the edges while huge gaps remain unbridged by evolution. And it is hardly unreasonable for creationists to point out that there are still two large gaps rather than one huge gap (see p. 126). The series of corresponding limbs (Figure 4, left) does not appear to show a clear progression. Even from looking at it, it is not obvious that the Panderichthys limb belongs in between the adjacent ones in the series. It has fewer small bones. And a later study indeed argued that Panderichthys’ fin may be closer to tetrapods in morphology than Tiktaalik., The Tiktaalik discoverers themselves appear to recognize that there are some anomalies: “In some features, Tiktaalik is similar to rhizodontids such as Sauripterus. These similarities, which are probably homoplastic, include the shape and number of radial articulations on the ulnare, the presence of extensive and branched endochondral radials, and the retention of unjointed lepidotrichia.” As explained in ch. 6, ‘homoplastic’ essentially means a common feature that can't be explained by inheritance from a common ancestor. But appealing to homoplasy is really explaining away evidence that doesn’t fit the paradigm, and indeed such explaining away is ubiquitous. Two proponents of evolution admit:

“Disagreements about the probable homologous or homoplastic nature of shared derived similarities between taxa lie at the core of most conflicting phylogenetic hypotheses.”

In fact, when more characteristics than just one are analyzed, homoplasies become even more necessary to explain away anomalies. Another example is that the neck region of Tiktaalik is said to be homoplastic with that of Mandageria

In reality, Tiktaalik appears to be another mosaic or chimera, like Archaeopteryx. It has some fish-like aspects, some unique features such as the hyomandibula, and some tetrapod-like features. Under an evolutionary scenario, this would mean that they are all at different stages of evolution. However, natural selection can only work on organisms as a whole, not on parts; therefore a new trait cannot be selected for outside of the context of the whole organism. Moreover, mosaic evolution does not identify an evolutionary lineage; evolution have only identified traits that seem to change in complex, independent and contradictory ways in an evolutionary framework. But a designer could create different creatures with different modules, that fit no consistent evolutionary pattern. This is contrary to Dawkins’ claim that there is “no borrowing” across different types of creatures unless there is a common ancestor which had the common feature (p. 297).

Transitional limb?

Cladogram of the pectoral fins on the tetrapod stem. From left to right: Glyptolepis, Sauripterus, Eusthenopteron,

Quite aside from the huge problems explaining the origin of locomotion, there are other problems. The series of corresponding limbs (Fig. above, right) does not appear to show the clear progression. Even from looking at it, it is not obvious that the Panderichthys limb belongs in between the adjacent ones in the series. It has fewer small bones. The authors themselves appear to recognize this:

‘In some features, Tiktaalik is similar to rhizodontids such as Sauripterus. These similarities, which are probably homoplastic, include the shape and number of radial articulations on the ulnare, the presence of extensive and branched endochondral radials, and the retention of unjointed lepidotrichia.’

‘Homoplastic’ essentially means ‘convergent’ or ‘analogous’, i.e. independently evolved because of a common function (such as the wings of pterosaurs, bats, birds and insects, according to evolutionists), rather than evolved from a common ancestor (homologous, as evolutionists claim for features such as the different forelimbs here). But homology is alleged to be the evidence for evolution (despite many problems—see Common structures = common ancestry?) But appeal to homoplasy is really explaining away evidence that doesn’t fit the paradigm, and indeed such explaining away is ubiquitous. Two proponents of evolution admit:

‘Disagreements about the probable homologous or homoplastic nature of shared derived similarities between taxa lie at the core of most conflicting phylogenetic hypotheses.’⁷

In fact, when more characteristics than just one are analysed, homoplasies become even more necessary to explain away anomalies, as will be explained in the section Mosaic rather than transitional.
Another major problem is that proponents of evolution appeal to the common pentadactyl 5-digit pattern as evidence for their common ancestry from a 5-digited creature. Yet the nearest creatures they have to a common ancestor did not have five digits! Acanthostega had eight, while Ichthyostega had seven.

Rather, it supports a particular subset of ID: the biotic message theory, as proposed by Walter ReMine in The Biotic Message. That is, the evidence from nature points to a single designer, but with a pattern which thwarts evolutionary explanations. In this case, the common modules point to one common designer, but evolution is powerless to explain this modular pattern, since natural selection can work only onorganisms as a whole. That is, it cannot select for particular head design as such, but only for creatures that have a head that confers superior fitness. But a designer who worked with different modules could create different creatures with different modules, that fit no consistent evolutionary pattern.

1) Sarfati : the greatest hoax on earth : page 115

The Deep Homology of the Autopod: Insights from Hox Gene Regulation 1

The evolution of tetrapod limbs from fish fins was a significant functional and morphological shift, but how significant was it in terms of the underlying genetic mechanisms? The fossil record provides insight into the morphological changes. However, to understand the underlying mechanisms, we must peer into the gene regulatory networks of living vertebrates. Analysis of HoxA/D expression in a basal actinopterygian, the North American paddlefish, Polyodon spathula, reveals patterns of expression long considered to be a unique developmental signature of the autopod (hands/feet, digits) and shown in tetrapods to be controlled by a “digit enhancer” regulatory landscape. These data, along with recent interspecific transgenic experiments, expression results from chondrichthyans, and data from fossils support the notion that the autopod shares a deep homology with the distal endoskeleton of the fin (distal radials) of other gnathostomes.

Introduction Fossils record the evolutionary transition from paired fins to paired limbs in sarcopterygian tetrapodomorphs during the latter half of the Devonian period . In recent years, our interpretation of the invasion of land by vertebrates has evolved somewhat—careful analysis of taxa close to the transition, such as Tiktaalik, Acanthostega , and Ichthyostega , support the notion of a unique and rather long-standing transitional ecology. Nonetheless, a major remodeling of many ancient vertebrate systems—for example, lateral lines, hearing, vision, jaw mechanics, structural support of the body and internal viscera, and unpaired and paired appendages—define this period as a major morphological event in vertebrate evolution. Within the paired appendages themselves, the origin of the autopod (hands, feet, and digits) is seen as one of the defining adaptations that make tetrapods unique. Here, we will address the origin and homology of the autopod by placing recent studies of gene expression and function in the context of datasets on fossils and comparative anatomy.

To evaluate possible changes in gene regulation that may associate with the fin-to-limb transition and the origin of the autopod, it is first necessary to phylogenetically bracket tetrapodomorph fish and stem tetrapods between living taxa that are amiable to developmental and genetic analysis (Fig. 1).



Fig. 1
Phylogenetic “bracketing” of the fin-to-limb transition (here represented by the tetrapodomorphs Sauripterus, Tiktaalik, and Acanthostega) with established (Danio, Mus) and emerging (Chondrichthyans, Polyodon) developmental model taxa.


(A) Skeletons of the pectoral fin and limbs highlighting hypothesized homologous regions.
(B) Summary of late-phase 5′ HoxD expression.
(C) Summary of late-phase 5′ HoxA expression. The condition for chondrichthyans has not yet been described. Anterior is left and distal is up in all illustrations.

Until recently, insights have primarily come from the use of established tetrapod (the mouse, Mus, and to a lesser extent the chicken, Gallus) and teleost (the zebrafish, Danio, and to a lesser extent the pufferfish, Fugu) genetic systems. These taxa provided the most powerful tools for functional assays and were already part of large and established communities in which techniques and results could be exchanged. It is also worth considering that these systems were not specifically chosen for their phylogenetic position, or to address evolutionary questions per se. However, a certain danger comes in bracketing a fossil transition with two highly derived clades, as when variation is present one cannot ascertain which character state is primitive. Outgroups are needed to polarize character states—for both morphology and developmental mechanisms.

Recently, more basal taxa of gnathostomes have come under scrutiny. Chief among these are a non-teleost actinopterygian, the North American paddlefish, Polyodon spathula (Davis et al. 2004a, 2007; Modrell et al. 2011), and chondrichthyan taxa for which eggs are readily available—the skate Raja erinacea (Dahn et al. 2007) and the catshark Scyliorhinus canicula (Tanaka et al. 2002; Freitas et al. 2007). With these additional taxa as outgroups, we can more effectively address the following questions: 


(1) What are the fundamental differences in gene expression and regulation between fins and limbs and 
(2) Do these differences offer insights into the origin of the autopod? In addition, we may ask whether the comparison of regulatory differences between fins and limbs can actually pinpoint the genetic changes behind this evolutionary transition.

Gene expression and functional studies demonstrate a remarkably conserved regulatory program for building paired appendages that may help elucidate homologous skeletal regions shared by fins and limbs. Among the genes that are best studied and best characterized are the Hox genes, which encode transcription factors that provide positional identity along animal axes, including the limbs (McGinnis and Krumlauf 1992). In general, Hox genes are arranged in genomic clusters, with multiple clusters present in vertebrates (Duboule 2007). All vertebrates possess two or more clusters of Hox genes, the result of a duplication event sometime after the evolutionary split of the vertebrate lineage from the rest of “invertebrate” bilaterian diversity, which possesses only a single Hox cluster (e.g., Drosophila). Two additional major duplication events of Hox clusters occurred within vertebrates: the first of these, resulting in four clusters (A–D), typify phylogenetically basal jawed fishes and tetrapods; and the second (resulting in eight ancestrally or seven due to subsequent loss of one cluster) characterizes the teleost lineage of actinopterygian fish (Prohanska and Stadler 2004). With these duplications came opportunity for the additional clusters to assume novel regulatory roles. For example, Hox clusters A and D became the key positional regulators of the development of appendages (unpaired and paired fins in fish, and limbs in tetrapods).
Hox genes exhibit a correspondence between their genomic position within a cluster and their domain of expression along the A-P axis of the embryo. The more 3′ (more telomeric) genes in a Hox cluster are expressed more anteriorly, and generally earlier, than more 5′ (more centromeric) genes of the cluster, a phenomenon known as spatial colinearity. This colinearity expresses itself not only during A-P patterning of the body but also in the patterning of the proximal to distal (P-D) and A-P axes of the appendages.

Experiments demonstrate that the conserved phenotypic pattern of tetrapod limbs (stylopod, zeugopod, and autopod regions) is clearly tied to Hox regulation during embryonic outgrowth of limb buds. In transgenic knockout mice, targeted deletion of individual Hox genes affects skeletal patterning in the specific region of the limb where that Hox gene would normally have been expressed (Davis et al. 1995). For example, double knockouts of HoxA11/D11 in combination result in severe truncation of the zeugopod. In wild-type mice, highest levels of HoxA11 and D11 would normally occur in the presumptive zeugopod (Davis and Capecchi 1996;Zákány et al. 1997). Similarly, an almost complete loss of the autopod (digits are lost, only the mesopodium remains) is observed inHoxA13/D13 double knockouts, the genes with the most distal expression within the limbs of wild-type mice (Fromental-Ramain et al. 1996).

A look at Hox A/D expression in fins and limbs reveals a biphasic pattern consisting of a phylogenetically conserved early phase during initial bud outgrowth, with some key differences specific to fins and limbs appearing as development proceeds. In the early buds of teleosts and tetrapods, 5′ Hox A/D members are expressed in a conserved, spatiotemporally collinear fashion. The more 5′ genes are progressively activated and then expressed in progressively restricted domains along the P-D and A-P axes, respectively. However, at later stages when the autopod is being specified, a distinct late-phase of 5′ HoxA/D expression with inverted spatial colinearity is activated along the A-P axis. This late phase, although once considered a unique developmental hallmark of autopod formation, does exhibit distinct expression patterns in tetrapods; these are not seen in other gnathostomes. For example, Hoxa11 and Hoxa13 resolve into mutually exclusive proximal and distal domains, with Hoxa13 expressed throughout the autopod. The late-phase has not been definitively confirmed in teleosts, and prior to the addition of more basal taxa (see sections below), it was proposed that the regulatory changes in Hox expression seen in teleosts and tetrapods may underlie the origin of the autopod (Sordino et al. 1995; Wagner and Chiu 2001). However, Ahn and Ho (2008) demonstrated a possible degraded or remnant late-phase expression for both HoxA and HoxD in zebrafish pectoral fins, a result further supported by the presence of late-phase enhancers in zebrafish capable of driving expression in the mouse autopod (Schneider et al. 2011, and the following section). These recent results, along with the simplified fin skeleton of teleosts (Davis et al. 2004a), suggest that teleosts may have lost, modified, or truncated portions of an ancestral Hox regulatory program that is retained in tetrapods. If so, teleosts may be poor proxies for the ancestral state of fin development.


Hox regulation of the development of appendages

In vivo chromosomal engineering studies in mice have offered much insight into the transcriptional regulation of biphasic HoxA/D expression in paired appendages. The HoxD cluster has been best characterized and will be the primary focus of our discussion here. Regulatory sequences sit outside of a tightly packed Hox cluster, flanking its 5′and 3′ends (Spitz et al. 2001; Fig. 2). Furthermore, the enhancers for early and late phases of HoxD expression consist of distinct and physically separated regulatory domains (Tarchini and Duboule 2006; Gonzalez et al. 2007).



Fig. 2 Regulation of early-phase and late-phase HoxD expression. 
(A) An Early Limb Control Region (ELCR) is hypothesized to drive temporal colinearity of early-phase HoxD. The time of transcriptional onset of a given Hox gene would be determined by the proximity to the gene to the ELCR, with more proximal genes having an earlier onset than do more distal ones. 
(B) Observed posterior restriction of more 5′ HoxD genes during the early-phase cannot be explained by the ELCR alone, supporting the existence of a second regulatory sequence (POST), centromeric to the cluster, that spatially restricts genes to more exclusive posterior domains based on their proximity to the regulatory sequence. Like the ELCR, POST has not been positively identified, but likely resides somewhere between Evx2 and the global control region (GCR; boxed area). 
(C) The CsB conserved region within the GCR, in association with 
(D), the CsC, promote expression of late-phase 5′ HoxD expression in the autopod. Two non-Hox genes, Lnp and Evx2, are also promoted in the autopod by CsB (and possibly CsC). A presumably ancestral HoxD14 gene has been identified in some basal taxa, including Polyodon (Crow et al. 2012). Expression patterns and possible functions for HoxD14 have not been described, and so the gene is left unregulated in this figure.

Early-phase HoxD appears to be regulated by an activation–inhibition interaction between sequences located on either side of the cluster. A 3′ (telomeric) early limb control region (ELCR; Fig. 2) is hypothesized to drive temporal colinearity of HoxD expression in the early bud (Zákány et al. 2004). Hox genes more proximal to the ELCR would be transcribed earlier in development than genes more distal to this control region. However, this mechanism alone does not explain the posterior restriction of more 5′ HoxD genes during the early phase. In a series of deletion experiments in mice, Tarchini and Duboule (2006) demonstrated that specific HoxD genes could be posteriorized in their pattern of expression by the removal of their 5′′Hox neighbors. From these results, they proposed that a distinct regulatory sequence (POST; Fig. 2), centromeric to the cluster, spatially restricts Hox genes to more exclusive posterior domains, again based on their proximity to the regulatory sequence. Although both the ELCR and POST regions remain poorly characterized, the mechanism does explain the temporal and spatial colinearity of early-phase expression.

Late-phase HoxD expression, associated with formation of the autopod, possesses a separate regulatory mechanism. Located 5′ (centromeric) of the cluster is the global control region (GCR; Fig. 2), which maps to the intergenic region between the ATP5G3 and Lunapark (Lnp) genes (Spitz et al. 2003). Within the GCR are two conserved regulatory domains, CsA and CsB. Of these, only the CsB region appears to contain limb-specific regulatory function. A further regulatory region (Prox) containing a conserved regulatory domain (CsC; Fig. 2) has also been identified, mapping to the intergenic region between Lnp and the gene Evx2.Gonzalez et al. (2007) demonstrated that neither CsB nor CsC alone could fully recapitulate normal autopod expression, suggesting a synergistic role for these two separate elements in regulating colinearity of late-phase HoxD expression from the 5′ side of the cluster. Thats clear evidence that both had to emerge together , since they are interdependent. It has also been observed that the two non-Hox genes that lie within the 5′ regulatory landscape,Lnp and Evx2, are also expressed in the mouse autopod, despite not having any clear functional role in autopod development. This demonstrates the lack of specificity in these 5′ enhancers—They promote a suite of genes (Lnp, Evx2, and HoxD) that are not structurally, functionally, or phylogenetically related to each other.

Early-phase and late-phase HoxD expression interact through the Sonic hedgehog pathway (Shh). ELCR-POST induced restriction of more 5′ HoxD genes into more exclusively restricted posterior domains within the bud sets up a unique posterior regulatory “compartment” that breaks Gli3-mediated symmetry of the early limb (Zákány et al. 2004). These unique populations of mesenchymal cells in the posterior bud are the only ones expressing the full compliment of HoxD transcription factors, inducing the localized expression of Shh transcripts and, thus, defining the zone of polarizing activity (ZPA). Shh expression in the ZPA then mediates, but is not mandatory for, late-phase expression in the autopod (Litingtung et al. 2002; te Welscher et al. 2002).

Recent experimental work by Sheth et al. (2012) provides additional insights into the role that Shh/Gli3 play in late-phase HoxD patterning of the autopod. Sheth and colleagues demonstrated that titration of 5′ HoxA/D genes from a Gli3 null mice results in increasing polydactyly, with increasingly thinner and more closely packed digits at the lowest Hox dosages. Intriguingly, the extreme phenotypes bear striking similarities to the radials of basal gnathostomes such as Polypterus (a basal actinopterygian) and chondrichthyans, suggesting that digit patterning may involve modification of an ancestral Turing-type reaction diffusion mechanism across the A-P extent of the appendage.


1) http://icb.oxfordjournals.org/content/early/2013/04/26/icb.ict029.full

Deep homology and the origins of evolutionary novelty 1

Do new anatomical structures arise de novo, or do they evolve from pre-existing structures? Advances in developmental genetics, palaeontology and evolutionary developmental biology have recently shed light on the origins of some of the structures that most intrigued Charles Darwin, including animal eyes, tetrapod limbs and giant beetle horns. In each case, structures arose by the modification of pre-existing genetic regulatory circuits established in early metazoans. The deep homology of generative processes and cell-type specification mechanisms in animal development has provided the foundation for the independent evolution of a great variety of structures.

The quest is that the genetic information has to be programmed to make the new structures, and, as stated above , the genetic regulatory circuits need also to be programmed. That is, two separate programs need to emerge, that is 1. the program which defines the physical structure, and 2. the program which knows where to find the genetic information in the genome, and when to express is during development. That are different layers of information, which must exist fully developed in order to make the limbs in question. 

It is not possible to identify what is new in evolution without understanding the old. This is a reflection of the way evolution works, with some novelties being traceable as modifications of primitive conditions and others having origins that are much less obvious. As a result, the problems of novelty and homology have been deeply intertwined for the past century and a half. It is here, at the interface between these two great concepts of evolutionary biology, where fresh data from developmental biology have had an extraordinary impact. One of the most important, and entirely unanticipated, insights of the past 15 years was the recognition of an ancient similarity of patterning mechanisms in diverse organisms, often among structures not thought to be homologous on morphological or phylogenetic grounds. In 1997, prompted by the remarkable extent of similarities in genetic regulation between organs as different as fly wings and tetrapod limbs, we suggested the term ‘deep homology’1 to describe the sharing of the genetic regulatory apparatus that is used to build morphologically and phylogenetically disparate animal features

This fact indeed was not a evolutionary prediction. Rather it confirms intelligent design, where the creator uses the same tools ( that is regulatory circuits ) to make different bodyparts.

http://reasonandscience.heavenforum.org/t2191-the-developmental-genetic-toolkit-and-the-molecular-homologyanalogy-paradox

Stephen C Meyer , Darwin's doubt pg.268:
This pattern contradicts the expectations of textbook evolutionary theory. Neo-Darwinism predicts that disparate adult structures should be produced by different genes. This prediction follows directly from the neo-Darwinian assumption that all evolutionary (including anatomical) transformations begin with mutations in DNA sequences—mutations that are fixed in populations by natural selection, genetic drift, or other evolutionary processes. The arrow of causality flows one way from genes (DNA) to development to adult anatomy. Thus, if biologists observe different animal forms, it follows that they should expect that different genes will specify those forms during animal development. Given the profound differences between the fruit-fly compound eye and the vertebrate camera eye, neo-Darwinian theory would not predict that the "same" genes would be involved in building different eyes in arthropods and chordates.

Homology, as classically defined, refers to a historical continuity in which morphological features in related species are similar in pattern or form because they evolved from a corresponding structure in a common ancestor. Deep homology also implies a historical continuity, but in this case the continuity may not be so evident in particular morphologies; it lies in the complex regulatory circuitry inherited from a common ancestor. In some instances, recognition of deep homologies can help in the identification of cryptic classical homologies, when morphological data alone are inadequate to make the case for homology. For example, the photoreceptors present in various extant clades would not be recognized as homologous without the observation of common underlying genetic cassettes. Deep homology, however, can also be found in contexts in which structures are not homologous in the classical sense. As we explored in 1997, appendages in vertebrates, arthropods and other bilaterians evolved independently, but their derivation was dependent on regulatory networks present in a common ‘urbilaterian’ ancestor. Most strikingly, the genetic regulatory cascade comprising a key transcription factor and downstream effector genes eliciting outgrowth (such as the Drosophila melanogaster gene Distal-less or its mouse homologue Dlx) seems to have been present in such a common ancestor and has been repeatedly used to control outgrowth formation in the protostome and deuterostome lineages3. Moreover, a series of deep homologies exist in the genetic systems used to pattern the appendages of vertebrates and arthropods, many of which have come to light since our original paper was written (for example, proximal-appendage specification by homothorax in D. melanogaster or its homologue Meis1 in mice4,5). The similarities are much more than the use of a common genetic tool kit of genes: they involve the use of genes and regulatory circuits that have previously evolved complex roles in an ancestral organism. Deep homology is important for the generation of novelties because ancient regulatory circuits provide a substrate from which novel structures can develop. In this Review, we explore three of Charles Darwin’s exemplars of evolution: animal eyes, tetrapod limbs and the giant horns of beetles. New data from studies of these features are offering surprising twists on classic examples of evolution. And, together, these examples illustrate how deep homology enables researchers to understand the generation of novelty in cases in which fossils are not informative; to make predictions about morphological transformation that can be tested by experimental and expeditionary work; and to see the extent to which common genetic mechanisms are used to generate diverse adaptations and can lead to the parallel evolution of novelties.


Tetrapod limbs and fish fins


In On the Origin of Species, Darwin wrote of the similarities of tetrapod limbs: “What can be more curious than that the hand of a man, formed for grasping, that of a mole for digging, the leg of the horse, the paddle of the porpoise, and the wing of the bat, should all be constructed on the same pattern, and should include similar bones, in the same relative positions?” The origin of limbs in the Devonian period allowed the invasion of land and the later evolution of vertebrates that could fly, dig, run, hop and climb. Consequently, tetrapod limbs are classic examples of evolutionary novelties 19,20. But they are also a prime example of homology: all tetrapod limbs have similar bone morphology and development, and this can be traced back to the limbs of Devonian vertebrates. As was clear to Darwin, this homology is immediately apparent in the detailed similarities of morphology and development of the bones in the limbs of all tetrapods. More controversial, however, have been attempts to compare these bones with those in the paired fins of fish. It is here where deep genetic homologies and the discovery of fossils conspire to offer fresh insights. The most striking differences between limbs and fins lie in the distal region of the appendage, as the pattern of the proximal bones is essentially identical among lobe-finned fish and tetrapods. Much of the surface area of fins is supported by dermal rays — bones that are completely absent in limbs. In place of these rays, limbs have a set of endochondral elements — the digits and wrist or ankle bones — that look unlike, and function differently from, fin radials. Importantly, these bones contain a series of characteristic joints that allow flexion and extension, particularly in those that enable a ‘palm’ area to lie flush with the ground. Tetrapods, then, have traded a dermal skeleton in the distal appendage for a complex endochondral one, and their evolved joints and bones allow the distal appendage to support the weight of the body. Genetic discoveries in the 1990s reinforced a classical view that digits, wrists and ankles have no direct correlate in fins. Developmental studies of Hoxd9, Hoxd10, Hoxd11, Hoxd12 and Hoxd13gene expression in tetrapod limbs revealed a discrete phase of expression directly associated with digital specification.  

There are four important features of this late-phase expression: first, expression occurs in a distal segment of the limb, the ‘paddle’, that does not overlap with more proximal zones; second, this expression occurs while the digits and mesopodial bones 



are being specified; third, the domains of expression of the 5ʹ Hoxd genes display ‘reverse colinearity’, such that Hoxd13 expres​sion(for example) extends more anteriorly than the expression domains of more 3ʹ genes; and fourth, late-phase expression is regulated independently from early-phase expression by a separate enhancer that drives distal expression. This distinct expression pattern of the Hoxd genes has been referred to as ‘phase 2 expression’. Phase 2 expression, with all the characteristics described above, was unknown in fish fins in the late 1990s, as the zebrafish (Danio rerio) was reported to have only a single phase of expression. The fossil record also seemed to support this conclusion, as the sister group to limbed vertebrates (pander ichthyids) seemed to lack any bones comparable to digits. Data from both types of study supported the idea that the origin of novelty at the morphological and functional levels would have happened in parallel to that at the genetic level. Just as for eyes, comparative data refined the hypothesis of novelty (Fig. 2).




Work on a variety of non-model vertebrates has revealed that a late phase of Hoxd expression exists in the distal fin bud. Indeed, it is now known to be a general feature of gnathostomes, having been discovered in basal actinopterygians, lungfish, zebrafish and a chondrichthyan. Although the details of late-phase patterns of expression vary between these taxa, some but not all aspects of the tetrapod phase 2 Hox pattern are present in fins. The most notable difference is that latephase expression in the fins of osteichthyans (paddlefish, zebrafish and lungfish) spatially overlaps with earlier phases of expression, whereas in tetrapods the phases of expression are segregated proximodistally such that phase 2, but not phase 1, expression is found in the autopod. Despite these differences, basal actinopterygians and lungfish have broad zones of expression that, like tetrapods, exhibit reverse colinearity.

The key question is whether these late phases of expression in tetrapod limbs and fish fins reflect the same process. There is, as yet, no evidence of independent regulation of the form described in tetrapods. Lacking this evidence, there are two tenable hypotheses: either fish have phase 2 expression homologous to that which specifies the digits in tetrapods, or the late-phase expression observed in fins is a temporal and spatial extension of a highly conserved early phase with unique dynamic properties in the fish. The two cases suggest different molecular scenarios for the origin of the autopod. If fish have true phase 2 Hox gene expression, the main difference between tetrapod limbs and fish fins lies not in the origin of late-phase Hox gene expression but in changes in the timing of this expression and/or in changes in genes acting downstream of the Hox genes that must have shaped the tetrapod form. Alternatively, if fish lack true phase 2 Hox gene expression, the evolution of the phase 2 regulatory module would be a unique and perhaps defining autopod invention of the tetrapod lineage. In either case, the evolutionary process reveals the impact of deep homology: different kinds of appendage arose by modifications to an ancient and conserved developmental system. Even if the morphological structures (fin rays and digits) are not homologous, there is deeper homology in the network of Hox genes and their targets within the limb or fin field, as well as in phase 2 regulation — if indeed it predated the evolution of the autopod.

The detection of deep homologies offers more than new glimpses of evolutionary history, however. Such homologies provide a profound insight into the evolutionary process. Studies of deep homology are showing that new structures need not arise from scratch, genetically speaking, but can evolve by deploying regulatory circuits that were first established in early animals. But herein lies a challenge for the next generation of biologists: if the mechanisms behind the formation of diverse organs are ancient and highly conserved, then parallel evolution must be considered a fact of life in the phylogenetic history of animals. With the growth of developmental genetics, it is possible to see beyond the view of homologies working at the level of whole organs. The mechanisms that define the ordinate axes of structures, the genetic circuits that pattern them, and the cell types with which organs are formed can be considered. The more that researchers look, the more they will find that the same tools have been used to build a great variety of structures long thought to have independent histories. Discerning what has been conserved and what is novel in the origins of organs and body plans will be possible only with more comparative data, experiments on non-model animals, and targeted fossil discoveries from crucial nodes in the tree of life.

1) http://www.nature.com/nature/journal/v457/n7231/full/nature07891.html

Expression of Hoxa-11 and Hoxa-13 in the pectoral fin of a basal ray-finned fish, Polyodon spathula: implications for the origin of tetrapod limbs 1

SUMMARY Paleontological and anatomical evidence suggests that the autopodium (hand or foot) is a novel feature that distinguishes limbs from fins, while the upper and lower limb (stylopod and zeugopod) are homologous to parts of the sarcopterygian paired fins. In tetrapod limb development Hoxa-11 plays a key role in differentiating the lower limb and Hoxa-13 plays a key role in differentiating the autopodium. It is thus important to determine the ancestral functions of these genes in order to understand the developmental genetic changes that led to the origin of the tetrapod autopodium. In particular it is important to understand which features of gene expression are derived in tetrapods and which are ancestral in bony fishes. To address these questions we cloned and sequenced the Hoxa-11 and Hoxa-13 genes from the North American paddlefish, Polyodon spathula, a basal ray-finned fish that has a pectoral fin morphology resembling that of primitive bony fishes ancestral to the tetrapod lineage. Sequence analysis of these genes shows that they are not orthologous to the duplicated zebrafish and fugu genes. This implies that the paddlefish has not duplicated its HoxA cluster, unlike zebrafish and fugu. The expression of Hoxa-11 and Hoxa-13 in the pectoral fins shows two main phases: an early phase in which Hoxa-11 is expressed proximally and Hoxa-13 is expressed distally, and a later phase in which Hoxa-11 and Hoxa-13 broadly overlap in the distal mesenchyme of the fin bud but are absent in the proximal fin bud. Hence the distal polarity of Hoxa-13 expression seen in tetrapods is likely to be an ancestral feature of paired appendage development. The main difference in HoxA gene expression between fin and limb development is that in tetrapods (with the exception of newts) Hoxa-11 expression is suppressed by Hoxa-13 in the distal limb bud mesenchyme. There is, however, a short period of limb bud development where Hoxa-11 and Hoxa-13 overlap similarly to the late expression seen in zebrafish and paddlefish. We conclude that the early expression pattern in tetrapods is similar to that seen in late fin development and that the local exclusion by Hoxa-13 of Hoxa-11 from the distal limb bud is a derived feature of limb developmental regulation.

INTRODUCTION
A major transition in vertebrate evolution was the origin of fully terrestrial animals, the tetrapods. One of the innovations that facilitated this transition from water to land was the tetrapod limb. Recent paleontological evidence suggests that the tetrapod limb originated about 360 million years ago (Mya) in aquatic animals living in shallow coastal waters (Clack 2002). At the morphological level the tetrapod limb arose from the paired sarcopterygian fins by the addition of a distal segment, the autopod, that is, the hand or foot . Hence a main objective for understanding the developmental evolution of tetrapods is to determine the changes in paired appendage development instrumental in the origin of the autopod. In tetrapod model organisms, that is, mouse, chick, and Xenopus, the development of the autopodium depends on the activity of sonic hedgehog (Shh) in the zone of polarizing activity and the expression of AbdB-like Hox genes from the HoxA and HoxD clusters. In the absence of Shh in the mouse, typical autopodial structures fail to develop. Lack of Shh activity in mouse also leads to a suppression of Hoxa-13 because of the presence of the repressor form of Gli3-protein. This regulatory link between Shh and Hoxa-13 expression appears to be ancestral. In the zebrafish Sonic-you mutant, which knocks out the Shh gene, expression of Hoxa- 13 is absent in the pectoral fin bud. Furthermore the deletion of the 50 HoxA and HoxD genes leads to the loss of autopodial structures, suggesting that Hoxa-13 acts upstream of the HoxD genes.

“Self-Regulation,” A New Facet of Hox Genes’ Function

Background: Precise temporal and spatial expression of the clustered Hox genes is essential for patterning the developing embryo. Temporal activation of Hox genes was shown to be cluster-autonomous. However, gene clustering appears dispensable for spatial colinear expression. Generally, a set of Hox genes expressed in a group of cells instructs these cells about their fate such that the differential expression of Hox genes results in morphological diversity. The spatial colinearity is considered to rely both on local and long-range cis regulation. Results: Here, we report on the global deregulation of HoxA and HoxD expression patterns upon inactivation of a subset of HOXA and HOXD proteins. Conclusions: Our data suggest the existence of a “self-regulation” mechanism, a process by which HOX proteins establish and/or maintain the spatial domains of the Hox gene family and we propose that the functionally dominant HOX proteins could contribute to generating the spatial parameters of Hox expression in a given tissue, i.e., HOX controlling the establishment of the ultimate HOX code.


We propose that the establishment of Hox expression patterns involves a “self-regulatory” mechanism whereby functionally dominant HOX proteins determine the spatial parameters of the other Hox genes’ expression in a given tissue. In this view, in animals, in which Hox genes are either clustered or nonclustered, the functionally dominant HOX protein ultimately establishes and/or maintains the spatial expression specificities or HOX code, eventually defining cell fate. 

Fossil data suggest that limbs evolved from fins, but how this morphological transformation occurred is not yet resolved (Cohn et al., 2002; Schneider and Shubin, 2013). Curiously, HoxA and HoxD cluster genes are expressed in overlapping domains in fins while the hallmark of tetrapod limbs is the segregation of Hox expression domains in the distal limb bud, at least in the species studied so far (Metscher et al., 2005; Woltering and Duboule, 2010). Segregation of Hox expression domains has been suggested as an important change in the evolution of well-articulated, functional tetrapod limbs (Metscher et al., 2005; Woltering and Duboule, 2010). The acquisition of new cis-regulatory elements modulating Hox expression or increased distal cell proliferation by prolonged AER function have been suggested as possible mechanisms involved in this evolutionary transformation (Sordino et al., 1995; Freitas et al., 2012; Schneider and Shubin, 2013). Recent studies in mice show that HoxA and HoxD genes are important for limb bud growth in addition to patterning (Kmita et al., 2005; Sheth et al., 2013). HOXD13 overexpression in zebrafish fins results in distal overgrowth, segregation of Hox domains and expression of markers specific to autopod (Freitas et al., 2012). Here we show that HOX13 proteins are important for the segregation of the other Hox domains along the P–D axis. Upon inactivation of HOX13, the other HoxA and HoxD genes are expressed in overlapping domains resembling Hox expression patterns in fish-fins. Therefore, we speculate that, in the course of evolution, acquisition of new cis-regulatory elements and/or modulation of AER signaling contributed to the distal specific expression of Hoxa13. In turn, distal expression of Hoxa13 ensured the expansion of autopod progenitors and generated the conditions required for segregation of the autopod and zeugopod domains of HoxA and HoxD genes, allowing for the development of the wrist and digits and thus giving rise to well-articulated, functional tetrapod limbs.

Genomic Regulation of Hox Collinearity 1

During vertebrate limb development, Hoxd genes are transcribed in two temporal phases; an early wave controls growth and polarity up to the forearm and a late wave patterns the digits. In this issue of Developmental Cell, Tarchini and Duboule (2006) report that two opposite regulatory modules direct early collinear expression of Hoxd genes.

Question : how could natural mechanisms have programmed and directed the right temporal phases of gene transcription of the right genes,  and early wave control ? Furthermore, the limbs develop at the right place, the right coordinates and positional information is required, they could develop anywhere on the body. Did natural mechanisms find out about the right place by trial and error ? There were myriads of positions possible to add the limb. How could the right and precise coordination of axial position be achieved by mutations ?  The problem is that nature has too many options and without design couldn’t sort them all out. Natural mechanisms are too unspecific to determine any particular outcome. Mutation and natural selection could theoretically form a new complex morphological feature like a  leg or a limb with the right size and form , and arrange to find out the right body location to grow them , but it could  also produce all kinds of other new body forms, and grow and attach them anywhere on the body, most of which have no biological advantage or are most probably deleterious to the organism. Natural mechanisms have no constraints, they could produce any kind of novelty. Its however that kind of freedom that makes it extremely unlikely that mere natural developments provide new specific evolutionary arrangements that are advantageous to the organism.  Nature would have to arrange almost a infinite number of trials and errors until getting a new positive  arrangement. Since that would become a highly  unlikely event, design is a better explanation. 

The vertebrate limb is a complex structure. The human forelimb, for example, contains 29 bones that are polarized along three axes: proximodistal (shoulder to fingertips),
anteroposterior (thumb to small finger) and dorsoventral (back of hand to palm). The limb skeleton develops from a simple bud of undifferentiated mesenchyme that belies its ultimate complexity. Transformation of a homogeneous population of cells into this elaborate network of structures involves establishment of positional information and translation of these coordinates into differentiation programs by cells in different parts of the bud (Wolpert, 1996).

Paramount to the orchestration of this process are the Hox genes, clustered transcription factors whose primary role  has been to pattern the head-to-tail axis. The origin of fins (the forerunners to tetrapod limbs) involved cooption of this axial patterning system to establish polarity and regulate growth of the appendages.

Hoxd genes are activated in two transcriptional waves that are associated with distinct early and late phases of limb development, when, respectively, proximal and distal structures are laid down (Nelson et al., 1996). They are deployed sequentially, in both time and space, with genes situated at the telomeric (30 ) end of the cluster
(e.g., Hoxd9) being expressed before, and anterior to, their centromeric (50 ) neighbors (e.g., Hoxd13). Over the course of limb development, these domains become dynamic, with different phases of expression corresponding to specific regions of the emerging limb skeleton. Hox gene expression adheres to the rules of collinear gene regulation, first described by Ed Lewis for the Drosophila Bithorax complex (Lewis, 1978). The phenomena of spatial and temporal collinearity have been recognized in vertebrate Hox genes for nearly two decades (Gaunt, 1988), but only recently have the genomic mechanisms underlying collinear transcription of the Hoxd complex been revealed. The late phase of Hoxd expression in the distal part of the limb controls development of the digits, and Duboule and colleagues have shown that a single enhancer (the ‘‘digit enhancer’’), embedded within a global control region (GCR), regulates the timing, spatial position, and quantitative levels of transcriptional activity (Kmita et al., 2002; Spitz et al., 2001; Za´ ka´ ny et al., 2004).

The transition from fish fins to tetrapod limbs involved development of a new set of structures, the digits, and the regulatory independence revealed here makes it unlikely that modulation of the ELCR played a role in this evolutionary innovation. Rather, the second wave of Hoxd transcription that controls digit formation may have been facilitated by evolution of a novel regulatory element, the digit enhancer (Spitz et al., 2001). Resolution of this evolutionary question will require a more detailed understanding of Hox gene expression, and the underlying regulation and genomic organization, in the fins of fishes at key phylogenetic positions, such as sharks and lungfishes.

1. http://www.evodevo.net/uploads/1/8/1/3/18132731/freitas_and_cohn.pdf
2. http://www.yale.edu/gpwagner/pdfs/Metscher05_pfishHoxa.pdf

Evolution of the Darwin Fish   1

For many years, Ichthyostega was the missing link between fish and four-footed land dwellers (tetrapods).  When Jennifer Clack discovered Acanthostega in 1991, it “changed this conception entirely,” says Neil H. Shubin in a review of Clack’s new book Gaining Ground, in Science Aug 8, 2003:

How do major shifts in evolution happen?  What is the way in which new designs and functions emerge [sic] over time?  Big transitions, like the origin of flight or the invasion of land, involve the evolution of new structures, functions, and ecological interactions.  Our understanding [sic] of the significant jumps in evolution has depended on a few relatively well-known intervals in the history of life.  The origin of tetrapods has been one of those exemplars, and in Gaining Ground Jennifer Clack provides a fresh look at this key evolutionary event.

(Emphasis added in all quotes).  Acanthostega had both gills and five-digit appendages.  According to Rubin, this set off a chain of discoveries around the world of putative missing links between sea-dwellers and land-dwellers.  Problems remain, however:

• Shubin speaks of the “new material that revealed that the current view of tetrapod origins was wrong in several important ways.”  For instance, “the origin of tetrapods was not necessarily linked to the invasion of land.”
  
  
  
• Of Acanthostega, he says, “Surprisingly, this primitive [sic] tetrapod retains a remarkable suite of aquatic adaptations, such as gills and flipper-like limbs.  These adaptations imply that fingers and toes first appeared[sic] in the paddle of an aquatic organism rather than in the hand or foot of a more terrestrial one.”  Yet digits appear in the flippers of aquatic mammals, and they are not presumed to be intermediates on the way to becoming land creatures, but quite the opposite.
  
  
  
• “Another big surprise came when Acanthostega and Ichthyostega were studied phylogenetically.”  It suggested more diversity than a simple monophyletic lineage between water and land.  Since then, a number of fossils have been found all over the world adapted to “different degrees of terrestriality.”  This “fossil bonanza has created a more complex view of what was formerly seen as a simple transformation.”
  
  
  
• Placing these fossils in relation to a phylogenetic tree is challenging, because “Descriptions of the osteological changes along the fish-to-tetrapod transition are relatively complicated because living taxa often lack comparable structures.”
  
  
  

We’ll let Shubin, an enthusiastic evolutionist, summarize the State of the Sea-Land Evolutionary Transition:

Where does Gaining Ground leave us?  New fossils, new phylogenetic hypotheses, and new discoveries from developmental genetics have exposed the complexity involved with the origin of novel taxa.  This complexity tells us much about how evolution works [sic].  As Clack demonstrates in the book, the tetrapod limb provides a major example of such evolutionary transformations.  The simple view would hold that the origin of tetrapods is associated with the invasion of land by vertebrates, the transformation of fins into limbs, and the origin of the first fingers and toes.  Clack shows that the relation among these three aspects is loose at best: primitive tetrapods are aquatic, primitive limbs can be very flipper-like, and digit-like structures appear in parallel in at least one other lineage of Devonian fish.  Indeed, transitional taxa are often mélanges of structures, genes, and functions seen in a variety of different primitive groups.  These mélanges are the result [sic] of parallel evolution and the disparate patterns of ecological and anatomical change.  The features that characterize important new groups often arise in several different primitive species independently.  In addition, major anatomical shifts can precede ecological ones.  In the case of tetrapods, key features evolved in fish living in aquatic ecosystems, and only later were they used to exploit terrestrial environments.  There are general lessons to be gleaned from this new view of tetrapod origins: the complex relation among parallel evolution, ecological change, and evolutionary diversification is likely to pertain to other evolutionary transitions as well.

Details on the book: Gaining Ground: The Origin and Evolution of Tetrapods by Jennifer A. Clack, Indiana University Press, Bloomington, IN, 2002.
What view do high school science students get?  The simple view.  The outdated view.  The wrong view.  Students are still being told about many simple, outdated, wrong views about the fossil record, the origin of life, natural selection and Darwin’s imaginary tree of life, as reported last month by Discovery Institute.  Here is another perfect example.  How many of you remember your high school biology textbook with a cartoon of a fish walking up onto the land?  That’s all it was – a cartoon.  It was Frank & Ernest material, unfit for the science lab.  (Now the cartoon has evolved into that occasional rear-bumper icon, the Darwin Fish.  Next time you see one, give the driver the URL to this story.)
    Jennifer Clack was one of the heroines in the PBS TV series Evolution.  In episode two, “Great Transformations” (in which Shubin also appeared), she showed off her prize fossil, while the series gave the impression here was a clear example of an evolutionary transitional form.  Don’t be fooled by the rhetoric.  Shubin is our hostile witness.
    We give an extended, uncut quote to avoid the common canard that critics of evolution quote out of context.  Shubin is clearly a staunch believer in evolution.  That makes his points all the more damaging to his beliefs.  It’s as if an Olympic coach admitted his team took illegal drugs, but it was OK, because everyone else did.  Rather than thinking this disqualifies the whole Olympics, he thinks his comeback makes the games better than ever.
    Notice how Shubin has just undermined the credibility of Darwinian evolution in this key event, this major shift in evolution as he labels it.  He starts out by asking how these transitions occur.  Asking the question implies that evolutionists don’t really know, a conclusion borne out by the rest of the review.  The tale hinges on relatively few well-known intervals, he says, of which the transition to land is one of the biggest and most well known.  Then he admits the old view is wrong!  New structures “emerge” (there’s that miracle word again) without regard to function.
    Why would a sea creature, living happily in the water, develop five-digit limbs if not to crawl out on the land?  Why not ask it if it wants to?  It apparently was happy where it was.  Have we learned nothing fromCoelacanth?  That famous fossil was supposedly evolving bony fins to support its weight on land, but is still doing just fine deep in the sea (a living fossil, once thought extinct since the dinosaurs).  It is found today swimming in upright positions feeding on the bottom, ostensibly with no desire to evolve into a salamander.  The same could be said for these extinct Devonian critters.  Only evolutionary belief puts them into a transition to tetrapods.
    Furthermore, consider these revelations by Shubin:

• The characteristics appear abruptly.
  
  
• They appear in parallel.  Darwin’s tree is not supposed to have parallel lines.  This multiplies the already near-miraculous improbabilities to have separate groups develop the same structures and functions simultaneously.
  
  
• The structures and functions have no clear relationship to one another, nor to the ecology.
  
  
• Many of the structures are not found in living counterparts, so their functions are inferred.
  
  
• Acanthostega has “a remarkable suite of aquatic adaptations.”  Evolutionary theory is supposed to explain adaptation, not assume it to be the product of evolution (circular reasoning).
  
  
• Transitional forms (a term that embeds Darwinian assumptions into the very words) are described as mélanges of structures, genes, and functions, i.e., mosaics of characteristics that do not sort easily into evolutionary lineages.  (Mélange, n.: “a mixture of incongruous elements.”)
  
  
• The “simple view” of the “few relatively well-known” intervals involving major transformations is wrong.  This view has been taught for decades, since at least 1928 with the discovery of Ichthyostega, long showcased as a classic example of a major evolutionary transformation.  Where is the retraction in the high school biology textbooks?
  
  
• “Major anatomical shifts can precede ecological ones,“ he says.  In other words, fish evolved the complexities of digitized limbs before they realized they could use them as feet on land.  So much for classical Darwinian theory.  This means that Acanthostega either had to simultaneously evolve digitized paddles and the muscles, brain cells, nerves, developmental pathways and know-how to use them, or else all of the above were freaks, as useless as tumors, that stayed around (leaving no fossil record) and were not eliminated by natural selection until their separate uselessnesses combined into a useful, functional, coordinated limb system that, without design, was later exploited by descendents as feet.
  
  

  “Well I’ll, be darned, Grandpa Acan, did you know I could use these things to walk on the land?  Gasp!  I can’t breathe!”
  

  
  
• It’s not only this transition that has the above problems.  He ends, “ the complex relation among parallel evolution, ecological change, and evolutionary diversification is likely to pertain to other evolutionary transitions as well.”  The whole shebang is a muddle.
  
  

What an implausible story.  (“Complex” is Shubin’s euphemism for “convoluted”.)  Only a believer could believe it.  There is no tree of evolution here, just a hodgepodge collection of fully-adapted, extinct animals.  The Darwinists thought they had a simple game of laying numbered coins in a row, but have been handed three-dimensional tic-tac-toe, checkers, chess pieces, Scrabble letters and dice by a jokester who challenges them to arrange them into an ancestral tree.  Just when they try to get a handle on that, the jokester dumps random pieces from dozens of different puzzles into the mix.  Nothing fazes them, though; they think they are making progress (just keep the funding flowing).
    So where does Gaining Ground leave us, really?  For one thing, throw out your high school evolutionary biology textbook.  It’s useless.  For another, stop waiting for the Darwinists to finish their game, or you’ll beLosing Ground.  Third, it’s hot outside.  Go take a swim with your digitized limbs.  If you have a tumor, maybe you can exploit it as scuba gear.

1)http://creationsafaris.com/crev0803.htm#fish30

HoxA and HoxD expression in a variety of vertebrate body plan features reveals an ancient origin for the distal Hox program 1

Background
Hox genes are master regulatory genes that specify positional identities during axial development in animals. Discoveries regarding their concerted expression patterns have commanded intense interest due to their complex regulation and specification of body plan features in jawed vertebrates. For example, the posterior HoxD genes switch to an inverted collinear expression pattern in the mouse autopod where HoxD13 switches from a more restricted to a less restricted domain relative to its neighboring gene on the cluster. We refer to this program as the ‘distal phase’ (DP) expression pattern because it occurs in distal regions of paired fins and limbs, and is regulated independently by elements in the 5′ region upstream of the HoxD cluster. However, few taxa have been evaluated with respect to this pattern, and most studies have focused on pectoral fin morphogenesis, which occurs relatively early in development.

Background
Hox genes are conserved, developmental regulatory genes that occur in all bilaterians. They are arranged in clusters and play a key role in animal development by specifying positional identities through nested and overlapping expression domains. This is referred to as ‘the Hox code’ and is accomplished through spatial, temporal, and quantitative collinearity. Collinear Hox expression, which has been described as ‘a spectacular phenomenon that has excited life scientists since its discovery in 1978′ [1], means that the order in which the genes occur on the chromosome is the order in which they are expressed in the organism [2,3], as defined by their anteriormost expression domain. During early animal development, collinear Hox expression sets up anterior-posterior patterning where the genes on the 3′ end of the cluster are expressed earlier in anterior domains, followed by the progressive and more posterior expression of genes located toward the 5′ end. The HoxA and HoxD genes are deployed in a similar manner during limb development to pattern the proximal limb, including the arm and forearm. An important distinction of collinear expression is that the 5′ genes have restricted expression domains relative to their 3′ neighbors on the cluster. This pattern of collinear Hox expression is sometimes called the ‘general Hox strategy,’ in part, because an alternative, inverted expression pattern has been observed with the 5′ (posterior) HoxD genes in distal regions of vertebrate fins and limbs. The latter is associated with a switch in cis-regulatory regions [4] from the telomeric side of the cluster (3′) to the centromeric side (5′) [5,6], and is manifest as a broader expression domain of the (5′) gene relative to its 3′ neighbor on the cluster. This unique expression pattern has been interchangeably referred to as ‘inverted’, ‘inverse’, ‘late-phase’, ‘autopodial-like’, or ‘reverse-collinear’ expression. Here, we refer to this pattern as ‘distal phase’ (DP) expression because it is associated with specification of distal structures and is regulated independently, but does not always follow an earlier collinear phase and is not solely associated with fins and limbs. To clarify, both proximal and distal expression patterns meet the definition of collinearity, but are differentiated with respect to their regulatory regions and the relative expression patterns of the genes in closest proximity to the active regulatory region.

Conclusions
The Hox DP expression pattern appears to be an ancient module that has been co-opted in a variety of structures adorning the vertebrate bauplan. This module provides a shared genetic program that implies deep homology of a variety of distally elongated structures that has played a significant role in the evolution of morphological diversity in vertebrates

1) http://www.evodevojournal.com/content/5/1/44

Other factors could be involved as well, including homeobox genes that are not Hox genes (that is, they do not affect the overall structure of an animal)....The drawback for scientists is that nature's shrewd economy conceals enormous complexity. Researchers are finding evidence that the Hox genes and the non-Hox homeobox genes are not independent agents but members of vast genetic networks that connect hundreds, perhaps thousands, of other genes. Change one component, and myriad others will change as well-and not necessarily for the better. Thus dreams of tinkering with nature's toolbox to bring to life what  scientists call a "hopeful monster"-such as a fish with feet-are  likely to remain elusive. Scientists, as Duboule observes, are still  far from reproducing in a laboratory the biochemical are that nature has accomplished." (J. Madeleine Nash, Chicago, "Where Do Toes Come From?", TIME, August 7,1995, p69)

Evolution and the Problem of Non-Functional Intermediates

Non-functionality and Irreducible Complexity: 
In the Origin of the Species, Charles Darwin said,"If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."¹In evolution, natural selection only preserves those structures which confer some advantage for the organism. If a structure isn't functional, then it confers no advantage, is a waste of the organism's resources, and will be selected out. Darwin says that there may exist structures for which functional intermediate stages would be impossible, i.e. the intermediates would not function. This is essentially the same challenge of irreducibly complex structures, where intermediate structures wouldn't be functional. Biologist Michael Behe explains:

"A system which meets Darwin's criterion [listed in the above quote] is one which exhibits irreducible complexity. By irreducible complexity I mean a single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced gradually by slight, successive modifications of a precursor system, since any precursor to an irreducibly complex system is by definition nonfunctional. Since natural selection requires a function to select, an irreducibly complex biological system, if there is such a thing, would have to arise as an integrated unit for natural selection to have anything to act on. It is almost universally conceded that such a sudden event would be irreconcilable with the gradualism Darwin envisioned."⁴In the quote above, Behe notes that there is a fundamental quality of any irreducibly complex system in that, "any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.”⁴ Behe elaborates upon this definition saying"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway."¹¹More than Just Behe?
Behe, who also compares the problem of functional intermediates to a "groundhog trying to cross a thousand lane highway,"⁹ is not alone in his sentiments. Many biologists see  the problem of non-functional intermediates to be a formidable challenge to Darwin's theory. 

Soren Lovtrup, professional biologist in Sweden, said


 "...the reasons for rejecting Darwin's proposal were many, but first of all that many innovations cannot possibly come into existence through accumulation of many small steps, and even if they can, natural selection cannot accomplish it, because incipient and intermediate stages are not advantageous."²


 Well known evolutionist vertebrate paleontologist Robert Carroll asked if the gradual processes of microevolution can evolve complex structures:"Can changes in individual characters, such as the relative frequency of genes for light and dark wing color in moths adapting to industrial pollution, simply be multiplied over time to account for the origin of moths and butterflies within insects, the origin of insects from primitive arthropods, or the origin of arthropods from among primitive multicellular organisms? How can we explain the gradual evolution of entirely new structures, like the wings of bats, birds, and butterflies, when the function of a partially evolved wing is almost impossible to conceive?"¹⁰To overcome the problems of non-functional intermediates, some biologists have proposed "macromutations" or "saltations" which would produce radically different organisms. Though Stephen Jay Gould is not a proponent of this theory, he noted that, "the absence of fossil evidence for intermediary stages between major transitions in organic design, indeed our inability, even in our imagination, to construct functional intermediates in many cases, has been a persistent and nagging problem for gradualistic accounts of evolution."⁸ Those who proposed that rare macromutations would produce "hopeful monsters", some of which might actually have some great advantage, have not been received well by biologists. Paleobiologists Douglas Erwin and James Valentine explain why:"Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable "hopeful monsters" ... render these explanations untenable."³Erwin and Valentine said this in regards to the origin of the major body plans of life--the phyla--and some marine classes, however, others have found other unevolvable structures. Turkish evolutionist Engin Korur says, "The common trait of the eyes and the wings is that they can only function if they are fully developed. In other words, a halfway-developed eye cannot see; a bird with half-formed wings cannot fly. How these organs came into being has remained one of the mysteries of nature that needs to be enlightened."⁵ 

Hox-Mutations or Miracle Mutations? 
Some biologists have also envisioned special mutations in regulatory homeobox or "Hox" genes, where simple mutations might be able to make large developmental changes in an organism which might case a radically different phenotype. However, manipulating "Hox" genes does little to solve the problem of generating novel functional biostructures, for making large changes in phenotype are rarely beneficial. Hox gene mutations may be a more simple mechanism for generating large change, but they also do not escape the problem of the "hopeful monster":"The drawback for scientists is that nature's shrewd economy conceals enormous complexity. Researchers are finding evidence that the Hox genes and the non-Hox homeobox genes are not independent agents but members of vast genetic networks that connect hundreds, perhaps thousands, of other genes. Change one component, and myriad others will change as well--and not necessarily for the better. Thus dreams of tinkering with nature's toolbox to bring to life what scientists call a "hopeful monster"- such as a fish with feet--are likely to remain elusive." ⁶The figure below explains:





Furthermore, many biologists forget when invoking Hox gene mutations that Hox genes can only re-arrange parts which are already there--they cannot create truly novel structures. An oversimplified discussion is that genes can be thought of in two categories: "master control genes" (Hox genes) and "body part genes." "Body part genes" code for actual body parts while "master control genes" tell those "body part genes" when and where to be expressed and create their respective part. However, Hox mutations will never create new "body part genes", and thus cannot add truly new phenotypic functions into the genome, and at best we are left with the quandaries associated with "pre-adaptation". The majority of evolutionary change must take place through evolving new "body part genes", which Hox mutations cannot do. One reviewer in Nature recognizes this fact:"Schwartz ignores the fact that homeobox genes are selector genes. They can do nothing if the genes regulated by them are not there. It is these genes that specify in detail the adaptive structure of the organs. To be sure, turning on a homeobox gene at the wrong place can result in the appearance of an ectopic organ, but only if the genes for that organ are present in the same individual. It is totally wrong to imply that an eye could be produced by a macromutation when no eye was ever present in the lineage before. Homeotic mutations that reshuffle parts do happen, and sometimes they may have led to fixation of real evolutionary novelties, but this does not mean that such changes are implied in the majority of speciations. In fact, macromutations of this sort are probably frequently maladaptive, in contrast to the vast number of past and present species-not to mention the fact that morphological differences between related species can be minute."⁷Biologist Jonathan Wells discusses the issue of Hox mutations in his book, Icons of Evolution, where he recognizes that while Hox genes can be manipulated to cause fruit flies to sprout legs from their head. Three specific mutations are necessary to create this mutant fruit fly, and the legs are not functional, and are unbeneficial to the organism. This is a great example of why meaningful Hox mutations are complex and less simple in generating large biological change than many have promised, and how the resulting phenotype would usually be useless and disadvantageous. 

Since this issue is fairly easy to understand, we'd like to just provide a couple of examples of both micro and macro-morphologies which we think are could not have functional intermediates. They defy any gradualistic Darwinian explanation, and seem to hold a level of complexity which at least very strongly implies an intelligent designer as their cause. 

Biological systems for which functional intermediates seem impossible: 


[*]Major pathways of metabolism

[*]Defense Mechanisms in Hawkmoths

[*]The vertebrate heart

[*]The DNA-Enzyme system

[*]The cognitive and physiological requirements for human speech

[*]Non-Functional Intermediates in Human Physiology 

References Cited:
1. Origin of the Species by Charles Darwin
2. Lovtrup, S. [professional biologist specialising in Systematics and Developmental Biology, Dept. Animal Physiology, University of Umee, Sweden (also headed the organization of Swedish Developmental Biologists from 1979-87] (1987), Darwinism: The Refutation of a Myth, Croom Helm Ltd., Beckingham, Kent, p. 275
3. Erwin, D..H., and Valentine, J.W. "'Hopeful monsters,' transposons, and the Metazoan radiation", Proc. Natl. Acad. Sci USA 81:5482-5483, Sept 1984
4. Michael Behe, from "Molecular Machines: Experimental Support for the Design Inference" available at "http://www.arn.org/docs/behe/mb_mm92496.htm".
5. Engin Korur, "Gozlerin ve Kanatlarin Sirri"(The Mystery of the Eyes and the Wings), Bilim ve Teknik, No 203, October 1984, p. 25.
6. Nash J.M., "Where Do Toes Come From?," Time, Vol. 146, No. 5, July 31, 1995. Also at "http://www.time.com/time/magazine/archive/1995/950731/950731.science.html"
7. Book review of Sudden Origins: Fossils, Genes, and the Emergence of Species by Jeffrey H. Schwartz (Wiley: 1999). by Eors Szathmary in Nature 399:24, June 1999 pg. 745. 
8. Stephen Jay Gould (1982), "Is a new and general theroy of evolution emerging?," In Maynard Smith, J. (ed.), Evolution now A century after Darwin. 129-145. Macmillan Press, London. 239 pp. First published (1980) Paleobiology, 6: 119-130.
9. Darwin's Black Box by Michael Behe, pg. 141-142. 
10. Robert Carroll, Patterns and Processes of Vertebrate Evolution, Cambridge: Cambridge University Press, 1997, pp. 8-10
11. A Response to Critics of Darwin's Black Box, by Michael Behe, PCID Vol 1.1, Jan/Feb/March 2002; ISCID.org. 
12. Lynch, M., Conery, J. S., "The Evolutionary Fate and Consequence of Duplicate Genes" Science 290:1151-1155 (Nov 10, 2000). 
13. Huges, Austin L., "Adaptive Evolution of Genes and Genomes". (see chapter 7, "Evolution of New Protein Function" pp 143-180. (Oxford University Press, New York, 1999). 

http://www.ideacenter.org/contentmgr/showdetails.php/id/841
14. Science and Creationism: A View from the National Academy of Sciences (2nd Ed, 1999; NAP).

The first tetrapods The first terrestrial vertebrates, able to walk on land, are found in the Devonian period and are known as tetrapods. The earliest specimens are thought to be Acanthostega and Ichthyostega (see diagrams in figure 5.2). To explain the transition from water to land the evolutionist must try to imagine what the gains were. Many thought that it could be as a result of pools drying up during droughts, thus encouraging changes in fish that would allow them to move on the shore to other pools. The problem with this is that the adaptations needed were for returning to water, not for living on the land. It is now thought that the enormous adaptations seen in the first tetrapods could not have been for just moving from dried pool to water. Instead it is now believed that the move to land was because of the available food on the shore line; that is the plants and the already existent terrestrial invertebrates. Pause for a moment and try to imagine the situation. Fish are in the water near the shore and there is food available on land if the fish can get out and walk (as well as breathe). As I detail the changes needed for such a transition, try to imagine how the multitude of presumed intermediate stages (on the way to becoming tetrapods) could have fared. We must remember that for Darwinian evolution to work there must be a clear survival advantage for the organism at every stage in its transition from one form to another. Every small change, presumed to be caused by random mutations, will only continue to be reproduced if the change causes an improvement. Remember too that the fish is already beautifully adapted to living in the water, where there is food available. There had to be some great advantage for it to abandon such an aquatic existence. Why should it do so? How could the first mutant fish that had half-fin and half-leg actually fare better than its cousins in the water? As we shall see, for any sort of reasonable life on land there had to be some extraordinary changes in fish anatomy and physiology but (and I emphasise this) it is hard to see how any intermediate stages from fin to legs could have had any survival advantage. Many palaeontologists feel that Acanthostega was only able to paddle in shallow water or on top of vegetation – rather than actually take its full weight on land. This does seem conjectural though and the Acanthostega limb is very different from the fin of a fish. There are no fossil intermediate stages of half fin/half leg but evolutionary theory has to believe that there were. Let us look at the details. A fish is supported by water and its body weight is effectively zero. On land, however, the body is held up by limbs. As a result of this the entire internal anatomy and skeleton of the tetrapod has to be changed to cope with the forces of gravity. For example, the vertebrae and their muscles had to become adapted to prevent the body sagging between the limbs. The ancestral, lobe-finned fish is thought to be of a group known as the osteolepiforms and a prime candidate now is one called Eusthenopteron. The collection of bones at the base of the fin has been described as comparable with the basic bones found in the tetrapod limb – that is humerus, ulna and radius. Such a connection is, however, fairly speculative – given that the shapes of the bones in the tetrapod limb are completely different, some of the lobefin bones do not get into the tetrapod limb and, most importantly, the tetrapod limb has a complicated arrangement of new wrist bones (ulnare, radiale and intermedium) as well as carpals, metacarpals and phalanges. The same problems exist for imagining the transition of the fish pelvic (rear) fin to hind limb. In order to become a tetrapod limb, the lobe fin required new bones, new joints and a completely new musculature and limb girdle. The limbs had to be used in an entirely different way from fins – requiring altered orientation and completely new neuromuscular co-ordination. The pectoral girdle in the fish is attached to the skull and that of the first and subsequent tetrapods is well behind the skull. The pelvic girdle in the fish is a small unit embedded in the body wall whereas that of the tetrapod is firmly attached to the vertebral column. The jaw hinge of the first tetrapod is also quite different from that of a fish. The transition to air breathing required the development of efficient lungs. It is postulated that the fish ancestor of tetrapods had lungs already – similar to the modern lungfish. There had to be loss of extra, unneeded fins (Eusthenopteron had two dorsal fins, an anal fin and a large tail fin). There also had to be a major change in the method of reproduction – it is postulated that the earliest tetrapods laid eggs in water and had an initial tadpole-like stage like our modern amphibians. Remember that this is quite unlike any stage in fish development and that to acquire an initial aquatic tadpole form which then developed limbs and emerged on land, is a huge macro leap in biological function. Try again to think through these changes, which all appear suddenly in the fossil record, and imagine how they could all have been harmonised, by entirely chance mutations, to give us the tetrapod on land that we see abruptly appearing in the fossil record. I believe that, once again, the Darwinist model fails us here.

The origin of evolutionary novelties: regulation of Hoxd genes and the evolutionary transition from fish fins to tetrapod limbs 

Analyses of molecular markers after the gain of function experiments suggested that the downstream Hoxd gene network required for these distal endoskeletal elaborations are present in zebrafish. Therefore, we infer that the last common ancestor of teleosts and tetrapods was already poised to expand the chondrogenic tissue distally. The acquisition of novel enhancers might have sufficed to initiate this process. 

How do they know ? Answer: They don't know. It's just speculation......

https://cordis.europa.eu/project/id/219621/reporting/it